Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques
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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
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Macaca mulatta
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Axilla skin Axillary skin,Skin of axilla,Axilla skin,axilla skin
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Microbiome measurement Microbiome measurement,microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 2013 sampling period
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 2015 sampling period
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The 2015 sampling period occurred from October 2015 through December 2015
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
- Group 1 sample size Number of subjects in the case (exposed) group
- 33
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
- Mann-Whitney (Wilcoxon)
- Welch's T-Test
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "sampling period" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.sampling period
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Fig 6, Text
Description: The volcano plot (center) depicts the differences between the 2013 and 2015 sampling periods for each detected ASV (red and black points). Taxa depicted in red are the most highly significant (P < 0.015). Overabundant ASVs from 2013 are located on the negative (left) side of the volcano plot, while overabundant ASVs from 2015 are located on the positive (right) side. The violin plots surrounding the volcano plot depict the CLR values of the most significant taxa from the volcano plot; left: overabundant taxa in 2013; right: overabundant taxa in 2015
Abundance in Group 1: increased abundance in 2015 sampling period
Revision editor(s): Fiddyhamma
Signature 2
Source: Fig 6, Text
Description: The volcano plot (center) depicts the differences between the 2013 and 2015 sampling periods for each detected ASV (red and black points). Taxa depicted in red are the most highly significant (P < 0.015). Overabundant ASVs from 2013 are located on the negative (left) side of the volcano plot, while overabundant ASVs from 2015 are located on the positive (right) side. The violin plots surrounding the volcano plot depict the CLR values of the most significant taxa from the volcano plot; left: overabundant taxa in 2013; right: overabundant taxa in 2015
Abundance in Group 1: decreased abundance in 2015 sampling period
| NCBI | Quality Control | Links |
|---|---|---|
| Cecembia | ||
| Nocardioides aestuarii | ||
| Paracoccus sp. (in: a-proteobacteria) | ||
| Rickettsiella sp. | ||
| Thauera aromatica |
Revision editor(s): Fiddyhamma
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-Core microbiome social group (R)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-Core microbiome social group (F)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The core features 1.0 list (e.g., features present in 100% of samples) was used to filter the complete microbiome table and output a “core” microbiome feature table, via q2-filter-features. The same core features were then removed from the complete microbiome table to output a “non-core” microbiome feature table. Core and non-core feature tables were then exported to biom format
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Core microbiome social groups (V)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Core microbiome social groups (F)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The core features 1.0 list (e.g., features present in 100% of samples) was used to filter the complete microbiome table and output a “core” microbiome feature table, via q2-filter-features.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-Core microbiome 2013 sampling period
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-Core microbiome 2015 sampling period
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The core features 1.0 list (e.g., features present in 100% of samples) was used to filter the complete microbiome table and output a “core” microbiome feature table, via q2-filter-features. The same core features were then removed from the complete microbiome table to output a “non-core” microbiome feature table. Core and non-core feature tables were then exported to biom format
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Core microbiome 2013 sampling period
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Core microbiome 2015 sampling period
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The core features 1.0 list (e.g., features present in 100% of samples) was used to filter the complete microbiome table and output a “core” microbiome feature table, via q2-filter-features.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Complete microbiome social group R
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Complete microbiome social group F
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colony members self-organize into social groups, demonstrate various forms of social behaviors, most notably grooming
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Fig 2B, text
Description: Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.
Abundance in Group 1: increased abundance in Complete microbiome social group F
| NCBI | Quality Control | Links |
|---|---|---|
| Cyanobacteriota |
Revision editor(s): Fiddyhamma
Signature 2
Source: Fig 2B, text
Description: Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.
Abundance in Group 1: decreased abundance in Complete microbiome social group F
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacillota | ||
| Pseudomonadota |
Revision editor(s): Fiddyhamma
Experiment 7
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Complete microbiome social group V
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Fig 2B, text
Description: Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.
Abundance in Group 1: decreased abundance in Complete microbiome social group V
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota |
Revision editor(s): Fiddyhamma
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Complete microbiome social group F
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Complete microbiome social group KK
- 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
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Fig 2B, text
Description: Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.
Abundance in Group 1: increased abundance in Complete microbiome social group KK
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Pseudomonadota |
Revision editor(s): Fiddyhamma
Experiment 9
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Complete microbiome social group V
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Fig 2B, text
Description: Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.
Abundance in Group 1: increased abundance in Complete microbiome social group V
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Fiddyhamma
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Complete microbiome social group HH
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Complete microbiome social group KK
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Fig 2B, text
Description: Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.
Abundance in Group 1: increased abundance in Complete microbiome social group KK
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota |
Revision editor(s): Fiddyhamma
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Complete microbiome social group V
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Fig 2B, text
Description: Box plots representing the taxonomic differences for specific phyla among social groups, with significance assessed using a KW test on CLR transformed relative abundance values: Actinobacteria (KW P = 0.00013), Cyanobacteria (KW P = 0.12), Firmicutes (KW P = 0.044), and Proteobacteria (KW P = 0.0096). Pairwise comparisons between groups were assessed using t-tests; the symbolic number coding of P-values is as follows: *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.001; ****, P ≤ 0.0001.
Abundance in Group 1: increased abundance in Complete microbiome social group KK
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota |
Revision editor(s): Fiddyhamma
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 2013 sampling period (Complete microbiome)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 2015 sampling period (Complete microbiome)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The 2015 sampling period occurred from October 2015 through December 2015
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
- Group 1 sample size Number of subjects in the case (exposed) group
- 33
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Figure 4B, text
Description: Box plots representing the significant pairwise taxa using Wilcoxon tests on CLR transformed relative abundance values on phyla: Actinobacteria, Firmicutes, Deinococcus-Thermus, Fusobacteria, and Proteobacteria.
Abundance in Group 1: decreased abundance in 2015 sampling period (Complete microbiome)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Pseudomonadota | ||
| Bacillota | ||
| Deinococcus | ||
| Fusobacteriia |
Revision editor(s): Fiddyhamma
