Differential Dynamics of the Ruminal Microbiome of Jersey Cows in a Heat Stress Environment/Experiment 2

From BugSigDB


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24

Curated date: 2023/10/23

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Subjects

Location of subjects
Republic of Korea
Host species Species from which microbiome was sampled. Contact us to have more species added.
Bos taurus
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Rumen Paunch,Rumen,rumen
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Ruminative stress response rumination,Ruminative stress response,ruminative stress response
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Jersey cows under normal condition
Group 1 name Corresponds to the case (exposed) group for case-control studies
Jersey cows under heat stress condition
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Jersey cows under heat stress condition. The measurement of the respiration rate and rectal temperature in May was considered as the normal condition, while measurement of the respiration rate and rectal temperature in August was considered the heat stress condition.
Group 0 sample size Number of subjects in the control (unexposed) group
8
Group 1 sample size Number of subjects in the case (exposed) group
8
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
none

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-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
3

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24

Curated date: 2023/10/23

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Source: figure 4C

Description: Differentially abundant taxa in Jersey cows under heat stress condition compared to Jersey cows under normal conditions

Abundance in Group 1: increased abundance in Jersey cows under heat stress condition

NCBI Quality ControlLinks
Bacillus cereus
Bacillus cereus group
Brachyspiraceae
Brachyspirales
Clostridium
Clostridium botulinum
Cyanobacteriota
Epsilonproteobacteria
Flavobacteriia
Fusobacteriia
Mollicutes
Mycoplasmatales
Mycoplasmatota
Sphingobacteriia
Staphylococcus
Tissierellia
Xanthomonas arboricola

Revision editor(s): Folakunmi, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24

Curated date: 2023/10/24

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Source: figure 4C + 4A

Description: Differentially abundant taxa in Jersey cows under heat stress condition compared to Jersey cows under normal conditions

Abundance in Group 1: decreased abundance in Jersey cows under heat stress condition

NCBI Quality ControlLinks
Actinomycetes
Actinomycetota
Bifidobacteriales
Coriobacteriia
Eubacteriales
Kitasatosporales
Micromonosporales
Pseudomonas
Pseudonocardiales
Streptomyces
Anaerorhabdus
Bacteroidales bacterium WCE2004

Revision editor(s): Folakunmi, ChiomaBlessing