Geography, niches, and transportation influence bovine respiratory microbiome and health/Experiment 1
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
- Population Population,population
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Nasopharyngeal swabs from Canada and bronchoalveolar lavage from Canada
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Nasopharyngeal swabs from China
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Nasopharyngeal swabs from two cities (Qiqihaer and Guangan) in China from the study of Cui et al (2021).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 127
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
- 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 nasopharyngeal samples (NPS) of China (Qiqihaer and Guangan) when compared with the nasopharyngeal samples of Saskatoon in Canada and bronchoalveolar lavage samples (BAL) of Alberta in Canada.
Abundance in Group 1: increased abundance in Nasopharyngeal swabs from China
Revision editor(s): Folakunmi, ChiomaBlessing
