Geography, niches, and transportation influence bovine respiratory microbiome and health
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
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
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Nasopharyngeal swabs from China and bronchoalveolar lavage from Canada
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Nasopharyngeal swabs from Saskatoon, Canada.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Nasopharyngeal swabs from Saskatoon in Canada from the study of Malmuthuge et al. (2021).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 33
- Group 1 sample size Number of subjects in the case (exposed) group
- 112
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: figure 2
Description: Differentially abundant taxa in the nasopharyngeal samples (NPS) of Saskatoon, Canada when compared with the NPS of China and bronchoalveolar lavage samples (BAL) of Alberta in Canada.
Abundance in Group 1: increased abundance in Nasopharyngeal swabs from Saskatoon, Canada.
Revision editor(s): Folakunmi, ChiomaBlessing
Experiment 3
Subjects
- 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
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
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
Experiment 4
Subjects
- 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
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
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
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- unloading after short distance transportation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- calves at the time of unloading from truck after 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
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Source: supplementary figure S4
Description: Signature microbiota in calves at the time of unloading from trucks after transportation at a short distance.
Abundance in Group 1: increased abundance in unloading after short distance transportation
| NCBI | Quality Control | Links |
|---|---|---|
| Rhizobium etli | ||
| Marinomonas sp. MED121 | ||
| Yoonia vestfoldensis |
Revision editor(s): Folakunmi
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 7 days after placement and adaptive feeding (short distance)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- calves 7 days after placement and adaptive feeding following 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.
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Source: supplementary figure S4
Description: calves 7 days after placement and adaptive feeding following transportation at short distance.
Abundance in Group 1: increased abundance in 7 days after placement and adaptive feeding (short distance)
| NCBI | Quality Control | Links |
|---|---|---|
| Dermacoccus sp. Ellin185 | ||
| Geotalea uraniireducens | ||
| Microscilla marina | ||
| Nocardiopsis dassonvillei | ||
| Spirosoma linguale | ||
| Streptomyces avermitilis |
Revision editor(s): Folakunmi, ChiomaBlessing
Experiment 7
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- before loading for long distance transportation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- calves before loading into truck for long distance transportation. 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 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- increased
Signature 1
Source: supplementary figure S4
Description: calves before loading for long distance transportation. 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.
Abundance in Group 1: increased abundance in before loading for long distance transportation
| NCBI | Quality Control | Links |
|---|---|---|
| Simonsiella muelleri | ||
| Methylobacterium radiotolerans | ||
| Pseudomonas fluorescens | ||
| Rhizorhabdus wittichii | ||
| Methylorubrum extorquens |
Revision editor(s): Folakunmi
Experiment 8
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- unloading from long distance transportation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- calves at the time of unloading from truck after long distance transportation. 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.
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- decreased
Signature 1
Source: supplementary figure S4
Description: abundant taxa in calves at the time of unloading from truck after long distance transportation. 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.
Abundance in Group 1: increased abundance in unloading from long distance transportation
Revision editor(s): Folakunmi
Experiment 9
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 7 days after placement and adaptive feeding(long distance)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- calves at 7 days after placement and adaptive feeding after long distance transportation. 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.
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- decreased
Signature 1
Source: supplementary figure S4
Description: abundant taxa in calves at 7 days after placement and adaptive feeding after long distance transportation. 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.
Abundance in Group 1: increased abundance in 7 days after placement and adaptive feeding(long distance)
Revision editor(s): Folakunmi, Davvve, ChiomaBlessing
Experiment 10
Subjects
- Location of subjects
- Canada
- 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 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
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)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- decreased
Signature 1
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
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
