Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease
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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.
- Homo sapiens
- 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,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Insulin sensitivity measurement insulin sensitivity test,Insulin sensitivity measurement,insulin sensitivity measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Insulin Sensitive (IS) Individuals
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Insulin Resistant (IR) Individuals
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals who are at risk for type 2 diabetes or voluntarily interested in diabetes-related research, whose steady-state plasma glucose (SSPG) was greater than or equal to 150 mg/dl after undergoing Glucose control assessments, comprising an annual oral glucose tolerance test and a gold-standard steady-state plasma glucose (SSPG) measurement.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- 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
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- date
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Table S1D + Figure S1M
Description: Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe)
Abundance in Group 1: increased abundance in Insulin Resistant (IR) Individuals
Revision editor(s): Joan Chuks, Adeitan
Signature 2
Source: Table S1D + Figure S1M
Description: Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe)
Abundance in Group 1: decreased abundance in Insulin Resistant (IR) Individuals
Revision editor(s): Joan Chuks
Experiment 2
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,skin of body
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
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
- increased
Signature 1
Source: Table S1D + Figure S1M
Description: Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe)
Abundance in Group 1: increased abundance in Insulin Resistant (IR) Individuals
Revision editor(s): Joan Chuks
Signature 2
Source: Table S1D + Figure S1M
Description: Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe)
Abundance in Group 1: decreased abundance in Insulin Resistant (IR) Individuals
Revision editor(s): Joan Chuks, Adeitan
Experiment 3
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Anterior naris Anterior nostril,Anterior naris,anterior naris
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table S1D
Description: Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe)
Abundance in Group 1: increased abundance in Insulin Resistant (IR) Individuals
Revision editor(s): Joan Chuks, Adeitan
Signature 2
Source: Table S1D
Description: Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe)
Abundance in Group 1: decreased abundance in Insulin Resistant (IR) Individuals
Revision editor(s): Joan Chuks
Experiment 4
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Posterior wall of oropharynx Posterior wall of oropharynx,posterior wall of oropharynx
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table S1D
Description: Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe)
Abundance in Group 1: increased abundance in Insulin Resistant (IR) Individuals
Revision editor(s): Joan Chuks
Signature 2
Source: Table S1D
Description: Taxa Differing in Abundance Between Insulin Sensitive and Insulin Resistant Individuals as determined by Linear discriminant analysis Effect Size (LEFSe)
Abundance in Group 1: decreased abundance in Insulin Resistant (IR) Individuals
Revision editor(s): Joan Chuks, Adeitan
