Current levels of microplastic pollution impact wild seabird gut microbiomes
Experiment 1
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Calonectris borealis
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Proventriculus , Cloaca Proventriculus,proventriculus,Cloacal chamber,Vent,Cloaca,cloaca
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Exposure Exposure,exposure
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- ASVs negatively correlated with microplastic count
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ASVs positively correlated with microplastic count
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ASVs positively correlated with microplastic count in Cory’s shearwaters (C. borealis) and Northern fulmars(F. glacialis).
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- N/A
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- 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).
- centered log-ratio
- Statistical test
- ANCOM
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Signature 1
Source: Figure 2(a)
Description: Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.
Abundance in Group 1: increased abundance in ASVs positively correlated with microplastic count
| NCBI | Quality Control | Links |
|---|---|---|
| Cetobacterium sp. | ||
| Corynebacterium xerosis | ||
| Ligilactobacillus aviarius | ||
| Parvimonas sp. |
Revision editor(s): Bolanle, Aleru Divine
Signature 2
Source: Figure 2(a)
Description: Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.
Abundance in Group 1: decreased abundance in ASVs positively correlated with microplastic count
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus sp. | ||
| Pseudoalteromonas sp. | ||
| Psychrobacter | ||
| Staphylococcus sp. | ||
| Psychrobacter sp. | ||
| Catellicoccus sp. |
Revision editor(s): Bolanle, Aleru Divine
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- ASVs negatively correlated with microplastic mass
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ASVs positively correlated with microplastic mass
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- ASVs positively correlated with microplastic mass in Cory’s shearwaters (C. borealis) and Northern fulmars(F. glacialis).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2(b)
Description: Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.
Abundance in Group 1: increased abundance in ASVs positively correlated with microplastic mass
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium sp. | ||
| Edwardsiella sp. (in: enterobacteria) | ||
| Pseudoalteromonas sp. | ||
| Catellicoccus sp. |
Revision editor(s): Bolanle, Aleru Divine
Signature 2
Source: Figure 2(b)
Description: Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.
Abundance in Group 1: decreased abundance in ASVs positively correlated with microplastic mass
| NCBI | Quality Control | Links |
|---|---|---|
| Cetobacterium sp. |
Revision editor(s): Bolanle, Aleru Divine
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Microplastic count and the Cloaca
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Microplastic count and the Proventriculus
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Interaction between Microplastic Count and the Proventriculus in Cory’s shearwaters (C. borealis) and Northern fulmars(F. glacialis).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 84
- Group 1 sample size Number of subjects in the case (exposed) group
- 85
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Figure 2(c)
Description: Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.
Abundance in Group 1: increased abundance in Microplastic count and the Proventriculus
| NCBI | Quality Control | Links |
|---|---|---|
| Edwardsiella sp. (in: enterobacteria) | ||
| Corynebacterium sp. |
Revision editor(s): Bolanle, Aleru Divine
Signature 2
Source: Figure 2(c)
Description: Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.
Abundance in Group 1: decreased abundance in Microplastic count and the Proventriculus
| NCBI | Quality Control | Links |
|---|---|---|
| Flaviflexus sp. |
Revision editor(s): Aleru Divine
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Microplastic mass and the Cloaca
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Microplastic mass and the Proventriculus
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Interaction between Microplastic mass and the Proventriculus in Cory’s shearwaters (C. borealis) and Northern fulmars(F. glacialis).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 2(d)
Description: Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.
Abundance in Group 1: increased abundance in Microplastic mass and the Proventriculus
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter sp. |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2(d)
Description: Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.
Abundance in Group 1: decreased abundance in Microplastic mass and the Proventriculus
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium perfringens |
Revision editor(s): Aleru Divine
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Microplastic count and Cory’s shearwaters (C. borealis)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Microplastic count and Northern fulmars(F. glacialis)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Interaction between Microplastic Counts and Northern fulmars(F. glacialis)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 58
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 2(e)
Description: Differentially abundant ASVs associated with microplastics (counts and mass) identified by ANCOM.
Abundance in Group 1: decreased abundance in Microplastic count and Northern fulmars(F. glacialis)
| NCBI | Quality Control | Links |
|---|---|---|
| Catellicoccus sp. |
Revision editor(s): Aleru Divine
