Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
- Uterine inflammatory disease inflammatory disease of the uterus,uterine inflammatory disease,Uterine inflammatory 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)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Cows with Metritis typically occurring within 21 days post-partum, characterized by an enlarged uterus, fever, and fetid, watery red-brown uterine discharge.
- 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
- 33
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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Table 1
Description: Most abundant genera for Metritis (MET regardless of antimicrobial treatment) vs. Control (CT)
Abundance in Group 1: increased abundance in Metritis group (MET)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Clostridium | ||
| Fusobacterium | ||
| Phocaeicola | ||
| Porphyromonas | ||
| Prevotella | ||
| Streptococcus |
Revision editor(s): MyleeeA
Signature 2
Source: Table 1
Description: Most abundant genera for Metritis (MET regardless of antimicrobial treatment) vs. Control (CT)
Abundance in Group 1: decreased abundance in Metritis group (MET)
| NCBI | Quality Control | Links |
|---|---|---|
| Dietzia | ||
| Microbacterium |
Revision editor(s): MyleeeA
Experiment 2
Subjects
- 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 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
Signature 1
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
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
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Clinical treatment Clinical treatment,clinical treatment
- 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
- Cows with metritis that had not received individual antimicrobial treatment in the last 14 days prior to sampling.
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
Lab analysis
Statistical Analysis
Signature 1
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_no Treatment when compared to control.
Abundance in Group 1: increased abundance in Metritis group (MET_no treatment)
Revision editor(s): MyleeeA
Signature 2
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_no Treatment when compared to control.
Abundance in Group 1: decreased abundance in Metritis group (MET_no treatment)
| NCBI | Quality Control | Links |
|---|---|---|
| Rathayibacter | ||
| Glutamicibacter | ||
| Pseudonocardia | ||
| Actinomycetota |
Revision editor(s): MyleeeA
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Uterine inflammatory disease inflammatory disease of the uterus,uterine inflammatory disease,Uterine inflammatory disease
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pus Cows
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Cows with purulent discharge (PUS); defined as a non-fetid purulent or mucopurulent vaginal discharge.
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
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 Pus when compared to control.
Abundance in Group 1: increased abundance in Pus Cows
| NCBI | Quality Control | Links |
|---|---|---|
| Gemmatimonadota | ||
| Chlorobiota | ||
| Chlamydiota | ||
| Bacteroidota | ||
| Liquorilactobacillus | ||
| Cyclobacterium | ||
| Owenweeksia | ||
| Anoxybacter | ||
| Flavihumibacter | ||
| Dyadobacter | ||
| Oceanobacillus |
Revision editor(s): MyleeeA
Signature 2
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 Pus when compared to control.
Abundance in Group 1: decreased abundance in Pus Cows
| NCBI | Quality Control | Links |
|---|---|---|
| Rathayibacter | ||
| Pseudonocardia | ||
| Glutamicibacter | ||
| Actinomycetota |
Revision editor(s): MyleeeA
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Clinical treatment Clinical treatment,clinical treatment
- 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
- Clinical group comparison of metritis or uterine health by other studies for Cows with metritis that had received individual antimicrobial treatment in the last 14 days prior to sampling.
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6 and Supplementary Table 3
Description: ANCOM-BC heatmap of natural log fold changes of genera abundance for MET_Treatment vs Control (CT) compared to genera from other studies.
Abundance in Group 1: increased abundance in Metritis group (MET_treatment)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptobacillus | ||
| Salmonella | ||
| Peptoniphilus | ||
| Pedobacter | ||
| Helicobacter | ||
| Filifactor | ||
| Cryptococcus | ||
| Citrobacter | ||
| Arcanobacterium | ||
| Anaerococcus |
Revision editor(s): MyleeeA
Signature 3
Source: Figure 6 and Supplementary Table 3
Description: ANCOM-BC heatmap of natural log fold changes of genera abundance for MET_Treatment vs Control (CT) compared to genera from other studies.
Abundance in Group 1: decreased abundance in Metritis group (MET_treatment)
Revision editor(s): MyleeeA
Experiment 6
Subjects
- 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 1 sample size Number of subjects in the case (exposed) group
- 25
Lab analysis
Statistical Analysis
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
