Differential Dynamics of the Ruminal Microbiome of Jersey Cows in a Heat Stress Environment
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Kim DH, Kim MH, Kim SB, Son JK, Lee JH, Joo SS, Gu BH, Park T, Park BY, Kim ET
Journal
Animals : an open access journal from MDPI
Year
2020
Keywords:
Holstein, Jersey, KEGG pathways, heat stress, ruminal microbiome
The microbial community within the rumen can be changed and shaped by heat stress. Accumulating data have suggested that different breeds of dairy cows have differential heat stress resistance; however, the underlying mechanism by which nonanimal factors contribute to heat stress are yet to be understood. This study is designed to determine changes in the rumen microbiome of Holstein and Jersey cows to normal and heat stress conditions. Under heat stress conditions, Holstein cows had a significantly higher respiration rate than Jersey cows. Heat stress increased the rectal temperature of Holstein but not Jersey cows. In the Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis, Jersey cows had a significantly higher proportion of genes associated with energy metabolism in the normal condition than that with other treatments. Linear discriminant analysis effect size (LEfSe) results identified six taxa as distinguishing taxa between normal and heat stress conditions in Holstein cows; in Jersey cows, 29 such taxa were identified. Changes in the rumen bacterial taxa were more sensitive to heat stress in Jersey cows than in Holstein cows, suggesting that the rumen mechanism is different in both breeds in adapting to heat stress. Collectively, distinct changes in rumen bacterial taxa and functional gene abundance in Jersey cows may be associated with better adaptation ability to heat stress.
Experiment 1
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
Experiment 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24
Differences from previous experiment shown
Subjects
- 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.
Lab analysis
Statistical Analysis
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
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
Revision editor(s): Folakunmi, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-24
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
Revision editor(s): Folakunmi, ChiomaBlessing
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