Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome/Experiment 4

From BugSigDB


Reviewed Marked as Reviewed by Svetlana up on 2025-3-20

Curated date: 2025/02/24

Curator: MyleeeA

Revision editor(s): MyleeeA, KateRasheed

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
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 0 sample size Number of subjects in the control (unexposed) group
32
Group 1 sample size Number of subjects in the case (exposed) group
31

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
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-3-20

Curated date: 2025/02/24

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Gemmatimonadota
Chlorobiota
Chlamydiota
Bacteroidota
Liquorilactobacillus
Cyclobacterium
Owenweeksia
Anoxybacter
Flavihumibacter
Dyadobacter
Oceanobacillus

Revision editor(s): MyleeeA

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-3-20

Curated date: 2025/02/24

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Rathayibacter
Pseudonocardia
Glutamicibacter
Actinomycetota

Revision editor(s): MyleeeA