Geography, niches, and transportation influence bovine respiratory microbiome and health/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-25
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 , Lung Nasenrachenraum,Epipharynx,Nasal part of pharynx,Pars nasalis pharyngis,Rhinopharynx,Nasopharynx,nasopharynx,Pulmo,Lung,lung
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sampling site Sampling site,sampling site
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Nasopharyngeal swabs from Canada and Nasopharyngeal swabs from China
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Bronchoalveolar lavage from Alberta, Canada
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Bronchoalveolar lavage collected from feedlot calves which died from bovine respiratory disease in Alberta, Canada from the study of Klima et al. (2019).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 130
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
- 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
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-25
Source: Figure 2
Description: Differentially abundant taxa in the bronchoalveolar lavage samples (BAL) of Alberta in Canada when compared with the nasopharyngeal samples (NPS) of China and NPS of Saskatoon, Canada .
Abundance in Group 1: increased abundance in Bronchoalveolar lavage from Alberta, Canada
Revision editor(s): Folakunmi, ChiomaBlessing
