Geography, niches, and transportation influence bovine respiratory microbiome and health/Experiment 10
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-28
Subjects
- Location of subjects
- Canada
- 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
- Nasopharynx Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breastfeeding duration , Transport Breastfeeding duration,breastfeeding duration,Transport,transport
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- suckling calves (control)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- weaning+short transportation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- These were the calves in the treatment group that got weaned and transported at short distance. Metagenomics of the bovine respiratory microbiome in treatment groups on days 0 (prior to weaning and short-distance transportation), 2, 4, 8, 14, and 28 was used to compare with the control group that stayed with their dams (suckling).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- none
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).
- raw counts
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-28
Source: figure 7
Description: Significantly abundant taxa in the weaning+short-transport group on day 14 when compared to the suckling group on day 14.
Abundance in Group 1: increased abundance in weaning+short transportation
| NCBI | Quality Control | Links |
|---|---|---|
| Mannheimia |
Revision editor(s): Folakunmi
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-28
Source: figure 7
Description: Significantly abundant taxa in the weaning+short-transport group on day 14 when compared to the suckling group on day 14.
Abundance in Group 1: decreased abundance in weaning+short transportation
| NCBI | Quality Control | Links |
|---|---|---|
| Moraxella |
Revision editor(s): Folakunmi
