Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome/Experiment 6
From BugSigDB
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
- Endometrial cavity Cavity of body of uterus,Endometrial cavity,Endometrial lumen,Intrauterine cavity,endometrial cavity
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Clinical treatment Clinical treatment,clinical treatment
- 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_no treatment)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Clinical group comparison of metritis or uterine health by other studies for Cows with metritis that had not 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
- 25
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
Source: Figure 6 and Supplementary Table 3
Description: ANCOM-BC heatmap of natural log fold changes of genera abundance for MET_no Treatment vs Control (CT) compared to genera from other studies.
Abundance in Group 1: increased abundance in Metritis group (MET_no treatment)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptobacillus | ||
| Filifactor | ||
| Citrobacter | ||
| Chlamydia |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 6 and Supplementary Table 3
Description: ANCOM-BC heatmap of natural log fold changes of genera abundance for MET_no Treatment vs Control (CT) compared to genera from other studies.
Abundance in Group 1: decreased abundance in Metritis group (MET_no treatment)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptomyces | ||
| Micrococcus | ||
| Corynebacterium | ||
| Brucella | ||
| Brevibacterium | ||
| Bifidobacterium |
Revision editor(s): MyleeeA
