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
Journal
Year
Pages:
First page:
Keywords:
Using the curatedMetagenomicData Biocondutor package (>=3.2.1): we calculated taxa prevalence of healthy adult control samples for each body site (including vagina, skin, feces, nasal cavity, milk, oral cavity) and at species/genus levels. Lists of typical healthy signatures are provided in this study by different thresholds of prevalence level.
For body site-typical microbiome signatures for children, please go to: https://bugsigdb.org/Study_608
Experiment 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/24
Subjects
- Location of subjects
- Italy
- Luxembourg
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- health study participation health questionnaire participation,health survey participation,health study participation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- healthy adult vagina 50% up
- Group 1 sample size Number of subjects in the case (exposed) group
- 96
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No
Lab analysis
- Sequencing type
- WMS
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- prevalence>50% Statistical test: "prevalence>50%" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/24
Source: 10.5281/zenodo.5565690
Description: healthy adult vagina genus >=50%
Abundance in Group 1:| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Revision editor(s): Haoyanzh
Experiment 2
Reviewed Marked as Reviewed by Lwaldron on 2022/08/25
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Skin of body Entire integument,Entire skin,Integument,Integumental organ,Pelt,Skin,Skin organ,Skin of body
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- none
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- healthy adult skin 50% up
- Group 1 sample size Number of subjects in the case (exposed) group
- 362
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- All records NA
Lab analysis
Statistical Analysis
- Statistical test
- prevalence>50% Statistical test: "prevalence>50%" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/25
Source: 10.5281/zenodo.5565690
Description: healthy adult skin genus >=50%
Abundance in Group 1:| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus | ||
| Cutibacterium | ||
| Enchelyodon sp. | ||
| Corynebacterium | ||
| Streptococcus | ||
| Micrococcus | ||
| Finegoldia | ||
| Moraxella | ||
| Rothia |
Revision editor(s): Haoyanzh
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2022/08/25
Source: 10.5281/zenodo.5565690
Description: healthy adult skin species in >=50% samples
Abundance in Group 1:Revision editor(s): Haoyanzh
Experiment 3
Reviewed Marked as Reviewed by Lwaldron on 2022/08/24
Differences from previous experiment shown
Subjects
- Location of subjects
- Australia
- Canada
- China
- Denmark
- Finland
- France
- Germany
- India
- Ireland
- Israel
- Italy
- Japan
- Luxembourg
- Netherlands
- South Korea
- Spain
- Switzerland
- United Kingdom
- United Republic of Tanzania
- United States of America
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- none - 50% prevalence threshold
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- feces from healthy adult
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- non-disease adult participants from curatedMetagenomicData
- Group 0 sample size Number of subjects in the control (unexposed) group
- 0
- Group 1 sample size Number of subjects in the case (exposed) group
- 9623
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- no (n=5572), yes (n=276)
Lab analysis
Statistical Analysis
- Statistical test
- prevalence > 50% Statistical test: "prevalence > 50%" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Source: 10.5281/zenodo.5565690
Description: healthy adult stool genus in >= 50% samples
Abundance in Group 1:Revision editor(s): Haoyanzh
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Source: 10.5281/zenodo.5565690
Description: healthy adult stool species in >=50% samples
Abundance in Group 1:Revision editor(s): Haoyanzh
Experiment 4
Reviewed Marked as Reviewed by Lwaldron on 2022/08/24
Differences from previous experiment shown
Subjects
- Location of subjects
- United States of America
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Nasal cavity Cavitas nasalis,Cavitas nasi,Cavity of nose,Cavity of olfactory apparatus,Cavum nasi,Nasal canal,Nasal conduit space,Nasal fossa,Nasal pit,Olfactory cavity,Olfactory chamber,Olfactory chamber cavity,Olfactory pit,Nasal cavity
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- nasal cavity from healthy adult
- Group 1 sample size Number of subjects in the case (exposed) group
- 92
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Unknown
Lab analysis
Statistical Analysis
- Statistical test
- prevalence > 50% Statistical test: "prevalence > 50%" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/25
Source: 10.5281/zenodo.5565690
Description: healthy adult nasal cavity genus in >=50% samples
Abundance in Group 1:| NCBI | Quality Control | Links |
|---|---|---|
| Cutibacterium | ||
| Staphylococcus | ||
| Corynebacterium | ||
| Malassezia |
Revision editor(s): Haoyanzh
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2022/08/25
Source: 10.5281/zenodo.5565690
Description: healthy adult nasal cavity species in >=50% samples
Abundance in Group 1:| NCBI | Quality Control | Links |
|---|---|---|
| Cutibacterium acnes | ||
| Staphylococcus epidermidis | ||
| Corynebacterium accolens | ||
| Malassezia restricta | ||
| Cutibacterium granulosum |
Revision editor(s): Haoyanzh
Experiment 5
Reviewed Marked as Reviewed by Lwaldron on 2022/08/25
Differences from previous experiment shown
Subjects
- Location of subjects
- Italy
- Philippines
- United States of America
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- oral cavity from healthy adult
- Group 1 sample size Number of subjects in the case (exposed) group
- 659
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No (n=16)
Lab analysis
Statistical Analysis
- Statistical test
- prevalence > 50% Statistical test: "prevalence > 50%" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Source: 10.5281/zenodo.5565690
Description: healthy adult oral cavity genus in >=50% samples
Abundance in Group 1:Revision editor(s): Haoyanzh
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2022/08/25
Source: 10.5281/zenodo.5565690
Description: healthy adult oral cavity species in >=50% samples
Abundance in Group 1:Revision editor(s): Haoyanzh
Experiment 6
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Differences from previous experiment shown
Subjects
- Location of subjects
- Italy
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Milk Mammary gland milk,Milk
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- milk from healthy adult
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Unknown
Lab analysis
Statistical Analysis
- Statistical test
- prevalence > 50% Statistical test: "prevalence > 50%" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Source: 10.5281/zenodo.5565690
Description: healthy adult milk genus in >=50% samples
Abundance in Group 1:| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Revision editor(s): Haoyanzh
Experiment 7
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Differences from previous experiment shown
Subjects
- Location of subjects
- Italy
- Luxembourg
- United States of America
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Not specified
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- healthy adult vagina 70% up
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Not specified
- 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
- 96
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No
Lab analysis
Statistical Analysis
- Statistical test
- prevalence>70% Statistical test: "prevalence>70%" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/25
Source: 10.5281/zenodo.5565690
Description: healthy adult vagina genus in >=70% samples
Abundance in Group 1:| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Revision editor(s): Haoyanzh
Experiment 8
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Skin of body Entire integument,Entire skin,Integument,Integumental organ,Pelt,Skin,Skin organ,Skin of body
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- none
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- healthy adult skin 70% up
- Group 1 sample size Number of subjects in the case (exposed) group
- 362
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- All records NA
Lab analysis
Statistical Analysis
- Statistical test
- prevalence>70% Statistical test: "prevalence>70%" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values.
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Source: 10.5281/zenodo.5565690
Description: healthy adult skin species in >=70% samples
Abundance in Group 1:| NCBI | Quality Control | Links |
|---|---|---|
| Cutibacterium acnes | ||
| Staphylococcus epidermidis | ||
| Malassezia restricta | ||
| Staphylococcus capitis | ||
| Cutibacterium granulosum |
Revision editor(s): Haoyanzh
Experiment 9
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Differences from previous experiment shown
Subjects
- Location of subjects
- Australia
- Canada
- China
- Denmark
- Finland
- France
- Germany
- India
- Ireland
- Israel
- Italy
- Japan
- Luxembourg
- Netherlands
- South Korea
- Spain
- Switzerland
- United Kingdom
- United Republic of Tanzania
- United States of America
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- none - 70% prevalence threshold
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- feces from healthy adult
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- non-disease adult participants from curatedMetagenomicData
- Group 0 sample size Number of subjects in the control (unexposed) group
- 0
- Group 1 sample size Number of subjects in the case (exposed) group
- 9623
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- no (n=5572), yes (n=276)
Lab analysis
Statistical Analysis
- Statistical test
- prevalence > 70% Statistical test: "prevalence > 70%" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Source: 10.5281/zenodo.5565690
Description: healthy adult stool genus in >= 70% samples
Abundance in Group 1:Revision editor(s): Haoyanzh
Signature 2
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Source: 10.5281/zenodo.5565690
Description: healthy adult stool species in >= 70% samples
Abundance in Group 1:Revision editor(s): Haoyanzh
Experiment 10
Reviewed Marked as Reviewed by Lwaldron on 2022/08/26
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- none - 0% prevalence threshold
Lab analysis
Statistical Analysis
- Statistical test
- prevalence &;amp;gt; 0% Statistical test: "prevalence &;amp;gt; 0%" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values.
Experiment 11
Reviewed Marked as Reviewed by Lwaldron on 2022/08/24
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- none - 30% prevalence threshold
Lab analysis
Statistical Analysis
- Statistical test
- prevelance > 30% Statistical test: "prevelance > 30%" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values.
Signature 1
Reviewed Marked as Reviewed by Lwaldron on 2022/08/24
Source: 10.5281/zenodo.5565690
Description: healthy stool genus prevalence >=30%
Abundance in Group 1:Revision editor(s): Haoyanzh
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