Differential Dynamics of the Ruminal Microbiome of Jersey Cows in a Heat Stress Environment/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24
Curated date: 2023/10/23
Curator: Folakunmi
Revision editor(s): Folakunmi, LGeistlinger, 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
- Response to heat response to heat shock,Response to heat,response to heat
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Holstein cows under normal condition
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Holstein cows under heat stress condition
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Holstein 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
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24
Source: figure 4B
Description: Differentially abundant taxa in Holstein cows under heat stress condition compared to cows under normal conditions
Abundance in Group 1: increased abundance in Holstein cows under heat stress condition
| NCBI | Quality Control | Links |
|---|---|---|
| Fibrobacteraceae | ||
| Fibrobacterales | ||
| Fibrobacteria | ||
| Fibrobacterota | ||
| Xanthomonas arboricola |
Revision editor(s): Folakunmi, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24
Source: figure 4B
Description: Differentially abundant taxa in Holstein cows under heat stress condition compared to cows under normal conditions
Abundance in Group 1: decreased abundance in Holstein cows under heat stress condition
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcaceae bacterium P7 |
Revision editor(s): Folakunmi, ChiomaBlessing
