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

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

Curated date: 2023/10/23

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

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 ControlLinks
Fibrobacteraceae
Fibrobacterales
Fibrobacteria
Fibrobacterota
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 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 ControlLinks
Ruminococcaceae bacterium P7

Revision editor(s): Folakunmi, ChiomaBlessing

Experiment 2


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

Curated date: 2023/10/23

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

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

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