Geography, niches, and transportation influence bovine respiratory microbiome and health/Experiment 4
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-28
Subjects
- 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
- Transport Transport,transport
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-transportation (control)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Before loading for short distance transportation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- calves before loading to truck for transportation at short distance. LefSe was used to identify the longitudinal changes of microbiota from the studies of Cui et al. (2021) and Malmuthuge et al. (2021), following transportation
- 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).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-28
Source: supplementary figure S4
Description: Signature microbiota in calves before loading into trucks for transportation at a short distance
Abundance in Group 1: increased abundance in Before loading for short distance transportation
| NCBI | Quality Control | Links |
|---|---|---|
| Nocardia farcinica | ||
| Idiomarina loihiensis | ||
| Streptomyces sp. e14 | ||
| Sodalis glossinidius |
Revision editor(s): Folakunmi
