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.
URI
Authors
Ange-Stark M, Parise KL, Cheng TL, Hoyt JR, Langwig KE, Frick WF, Kilpatrick AM, Gillece J, MacManes MD, Foster JT
Journal
Microbiology spectrum
Year
2023
Keywords:
Eptesicus fuscus, Myotis lucifugus, Perimyotis subflavus, Pseudogymnoascus destructans, bat populations, disease ecology, microbiome, white-nose syndrome
Inherent complexities in the composition of microbiomes can often preclude investigations of microbe-associated diseases. Instead of single organisms being associated with disease, community characteristics may be more relevant. Longitudinal microbiome studies of the same individual bats as pathogens arrive and infect a population are the ideal experiment but remain logistically challenging; therefore, investigations like our approach that are able to correlate invasive pathogens to alterations within a microbiome may be the next best alternative. The results of this study potentially suggest that microbiome-host interactions may determine the likelihood of infection. However, the contrasting relationship between Pd and the bacterial microbiomes of Myotis lucifugus and Perimyotis subflavus indicate that we are just beginning to understand how the bat microbiome interacts with a fungal invader such as Pd.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Myotis lucifugus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Skin epidermis Epidermis,Skin,Vertebrate epidermis,Skin epidermis,skin epidermis
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Fungal infectious disease fungal infection,Fungi caused disease or disorder,Fungi disease or disorder,Fungi infection,Fungi infectious disease,infection, fungal,infections, Fungi,mycoses,mycosis,Fungal infectious disease,fungal infectious disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pseudogymnoascus Destructans (PD) Negative
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Pseudogymnoascus Destructans (PD) positive
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Myotis lucifugus Bats species infected with Pseudogymnoascus destructans (Pd).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 81
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).
- relative abundances
- Statistical test
- LEfSe
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Source: Results Text and Fig 4
Description: Taxonomic differential abundance analyses in Pseudogymnoascus destructans (Pd)-positive and Pseudogymnoascus destructans (Pd)-negative M. lucifugus.
Abundance in Group 1: increased abundance in Pseudogymnoascus Destructans (PD) positive
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudonocardiaceae |
Revision editor(s): MyleeeA
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Source: Results Text and Fig 4
Description: Taxonomic differential abundance analyses in Pseudogymnoascus destructans (Pd)-positive and Pseudogymnoascus destructans (Pd)-negative M. lucifugus.
Abundance in Group 1: decreased abundance in Pseudogymnoascus Destructans (PD) positive
| NCBI | Quality Control | Links |
|---|---|---|
| Brucellaceae | ||
| Chromatiales | ||
| Cytophagaceae | ||
| Rhizobiaceae |
Revision editor(s): MyleeeA
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Differences from previous experiment shown
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Perimyotis subflavus
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Perimyotis subflavus Bats species infected with Pseudogymnoascus destructans (Pd).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
- Group 1 sample size Number of subjects in the case (exposed) group
- 95
Lab analysis
- Sequencing type
- ITS / ITS2
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- decreased
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Differences from previous experiment shown
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Myotis lucifugus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Batsskin swaps
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Substrate (Environmental swaps)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Substrate swab samples simultaneously collected from the ceiling or walls of each hibernaculum at least 10 cm from the bat species.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 154
- Group 1 sample size Number of subjects in the case (exposed) group
- 70
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Source: Figure S8
Description: Bacterial differential abundance between bat and substrate samples.
Abundance in Group 1: increased abundance in Substrate (Environmental swaps)
Revision editor(s): MyleeeA
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Source: Figure S8
Description: Bacterial differential abundance between bat and substrate samples.
Abundance in Group 1: decreased abundance in Substrate (Environmental swaps)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadaceae | ||
| Enterobacteriaceae | ||
| Micrococcaceae | ||
| Staphylococcaceae | ||
| Caryophanaceae | ||
| Carnobacteriaceae | ||
| Streptococcaceae |
Revision editor(s): MyleeeA
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