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

Curated date: 2023/10/23

Curator: Folakunmi

Revision editor(s): WikiWorks, LGeistlinger, ChiomaBlessing, Folakunmi, KateRasheed

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

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, WikiWorks

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

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Fibrobacteraceae
Fibrobacterales
Fibrobacteria
Fibrobacterota
Xanthomonas arboricola

Revision editor(s): Folakunmi, ChiomaBlessing, WikiWorks

Signature 2

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

Curated date: 2023/10/24

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing, WikiWorks

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

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Ruminococcaceae bacterium P7

Revision editor(s): Folakunmi, ChiomaBlessing, WikiWorks

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2023/10/23

Curator: Folakunmi

Revision editor(s): WikiWorks, ChiomaBlessing, Folakunmi, KateRasheed

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.

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, WikiWorks

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 Control	Links
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, WikiWorks

Signature 2