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

Study information

Needs review

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

32630754

DOI Digital object identifier for electronic documents.

https://doi.org/10.3390/ani10071127

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

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Curated date: 2023/10/23

Curator: Folakunmi

Revision editor(s): Folakunmi, LGeistlinger

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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: response to heat response to heat shock,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

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

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Curated date: 2023/10/23

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Source: figure 4B

Description: Differentially abundant taxa in Holstein cow under heat stress condition

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

NCBI	Quality Control	Links
Fibrobacteria
Fibrobacterales
Fibrobacteraceae
Fibrobacterota
Xanthomonas arboricola

Revision editor(s): Folakunmi

Signature 2

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Curated date: 2023/10/24

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Source: figure 4B

Description: Differentially abundant taxa in Holstein cow under heat stress condition

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

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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

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

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): Not specified

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Not specified

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: Not specified

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

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/10/23

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: figure 4C

Description: Differentially abundant taxa in Jersey cow under heat stress condition.

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

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