Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2025-3-20
Subjects
- Location of subjects
- United States of America
- 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
- Endocervix Endocervix,endocervix
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Uterine disease disease of uterus,disease or disorder of uterus,disorder of uterus,uterine disease,uterine disorder,uterus disease,uterus disease or disorder,Uterine disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control group (CT)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Metritis group (MET_treatment)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Cows with metritis that had received individual antimicrobial treatment in the last 14 days prior to sampling.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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).
- log transformation
- Statistical test
- ANCOM-BC
- 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)?
- Yes
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-3-20
Source: Figure 4 and 5
Description: Heatmap of natural log fold changes in abundance of the phyla and genera with an adjusted p<0.05 for MET_Treatment when compared to control.
Abundance in Group 1: increased abundance in Metritis group (MET_treatment)
Revision editor(s): MyleeeA
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-3-20
Source: Figure 4 and 5
Description: Heatmap of natural log fold changes in abundance of the phyla and genera with an adjusted p<0.05 for MET_Treatment when compared to control.
Abundance in Group 1: decreased abundance in Metritis group (MET_treatment)
Revision editor(s): MyleeeA
