Current levels of microplastic pollution impact wild seabird gut microbiomes
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Fackelmann G, Pham CK, Rodríguez Y, Mallory ML, Provencher JF, Baak JE, Sommer S
Journal
Nature ecology & evolution
Year
2023
Microplastics contaminate environments worldwide and are ingested by numerous species, whose health is affected in multiple ways. A key dimension of health that may be affected is the gut microbiome, but these effects are relatively unexplored. Here, we investigated if microplastics are associated with changes in proventricular and cloacal microbiomes in two seabird species that chronically ingest microplastics: northern fulmars and Cory's shearwaters. The amount of microplastics in the gut was significantly correlated with gut microbial diversity and composition: microplastics were associated with decreases in commensal microbiota and increases in (zoonotic) pathogens and antibiotic-resistant and plastic-degrading microbes. These results illustrate that environmentally relevant microplastic concentrations and mixtures are associated with changes in gut microbiomes in wild seabirds.
Experiment 1
Subjects
- Location of subjects
- Portugal
- 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
- Proventricular microbiome in Cory's sheawater individuals
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cloacal microbiome in Cory's sheawater individuals
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- effect of microplastic count in the Cloacal microbiome in Cory's sheawater individuals
- Group 0 sample size Number of subjects in the control (unexposed) group
- 85
- Group 1 sample size Number of subjects in the case (exposed) group
- 84
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
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
Description: Differential abundance of microplastic counts
Abundance in Group 1: increased abundance in Cloacal microbiome in Cory's sheawater individuals
| NCBI | Quality Control | Links |
|---|---|---|
| Cetobacterium |
Revision editor(s): Bolanle
Signature 2
Source: figure 2
Description: Differential abundance of microplastic counts
Abundance in Group 1: decreased abundance in Cloacal microbiome in Cory's sheawater individuals
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium sp. | ||
| Edwardsiella | ||
| Pseudoalteromonas sp. | ||
| catellicoccuscatellicoccus |
Revision editor(s): Bolanle
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- abundance of microplastic mass in proventriculus
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- abundance of microplastic mass in cloaca
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- effect of in microplastic mass in c. borealis
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
Description: Differential abundance associated with microplastic mass
Abundance in Group 1: increased abundance in abundance of microplastic mass in cloaca
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus sp. | ||
| Pseudoalteromonas sp. | ||
| Psychrobacter sp. PRwf-1 | ||
| Staphylococcus sp. | ||
| CatellicoccusCatellicoccus |
Revision editor(s): Bolanle
Signature 2
Source: figure 2
Description: Differential abundance associated with microplastic mass
Abundance in Group 1: decreased abundance in abundance of microplastic mass in cloaca
| NCBI | Quality Control | Links |
|---|---|---|
| Cetobacterium | ||
| Corynebacterium sp. | ||
| Ligilactobacillus aviarius | ||
| Parvimonas sp. |
Revision editor(s): Bolanle
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- abundance of microplastic count and mass in cory's shearwaters
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- abundance of microplastic count and mass in nothern fulmars
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- effect of microplastic count and mass in proventriculus and cloaca in seabirds
- 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
Description: Differential abundance associated with microplastic mass
Abundance in Group 1: decreased abundance in abundance of microplastic count and mass in nothern fulmars
| NCBI | Quality Control | Links |
|---|---|---|
| catellicoccuscatellicoccus | ||
| Clostridium perfringens | ||
| Acinetobacter sp. |
Revision editor(s): Bolanle
Experiment 4
Differences from previous experiment shown
Subjects
- Location of subjects
- Canada
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Fulmarus glacialis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Proventricular microbiome in nothern fulmars individuals
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cloacal microbiome in nothern fulmars individuals
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- effect of microplastic count in the Cloacal microbiome in nothern fulmars individuals
- Group 0 sample size Number of subjects in the control (unexposed) group
- 85
- Group 1 sample size Number of subjects in the case (exposed) group
- 84
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
Experiment 5
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- abundance of microplastic mass in proventriculus
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- abundance of microplastic mass in cloaca
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- effect of microplastic mass in 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
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