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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 (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- randomly selected never smokers with cotinine <0.05 ng/mL
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- self-reported current cigarette smokers with the highest serum cotinine
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Associations with tobacco use
- Group 0 sample size Number of subjects in the control (unexposed) group
- 13
- Group 1 sample size Number of subjects in the case (exposed) group
- 77
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 5 days
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
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age, education level, race, sex, Matched on: "income" is not in the list (abdominalhernia, abnormal glucose tolerance, accute-on-chronic liver failure, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, ...) of allowed values.income, Matched on: "nativity" is not in the list (abdominalhernia, abnormal glucose tolerance, accute-on-chronic liver failure, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, ...) of allowed values.nativity
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Spreadsheet
Description: The relative abundance of selected species in former, second hand, alternative and never smokers.
Abundance in Group 1: increased abundance in self-reported current cigarette smokers with the highest serum cotinine
Revision editor(s): Kelvin Joseph
Signature 2
Source: Spreadsheet
Description: The relative abundance of selected species in former, second hand, alternative and never smokers
Abundance in Group 1: decreased abundance in self-reported current cigarette smokers with the highest serum cotinine
Revision editor(s): Kelvin Joseph
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- smoking behavior smoking,smoking behavior
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Females that have never smoked
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Females who have smoked before
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Females who have smoked before
- 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
- 3
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Spreadsheet
Description: The relative abundance of selected species in former, second hand, alternative and never smokers
Abundance in Group 1: increased abundance in Females who have smoked before
NCBI | Links |
---|---|
NANA |
Revision editor(s): Kelvin Joseph
Signature 2
Source: Spreadsheet
Description: The relative abundance of selected species in former, second hand, alternative and never smokers
Abundance in Group 1: decreased abundance in Females who have smoked before
NCBI | Links |
---|---|
Actinobacillus | |
Lactobacillus � |
Revision editor(s): Kelvin Joseph
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- randomly selected never smokers with cotinine <0.05 ng/mL
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- self-reported current cigarette smokers with high serum cotinine
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- individuals with smoking behavior belonging to the age group of 35-65 and over
- Group 1 sample size Number of subjects in the case (exposed) group
- 55
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Spreadsheet
Description: The relative abundance of selected species in former, second hand, alternative and never smokers
Abundance in Group 1: increased abundance in self-reported current cigarette smokers with high serum cotinine
NCBI | Links |
---|---|
Bifidobacterium � | |
Capnocytophaga � | |
Lactobacillus � | |
Lactococcus � | |
Leptotrichia � | |
Porphyromonas � | |
Prevotella � | |
Rothia � | |
Scardovia � | |
Streptococcus � |
Revision editor(s): Kelvin Joseph
Signature 2
Source: Spreadsheet
Description: The relative abundance of selected species in former, second hand, alternative and never smokers
Abundance in Group 1: decreased abundance in self-reported current cigarette smokers with high serum cotinine
Revision editor(s): Kelvin Joseph
Experiment 4
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- people with some college or associate degree or high school diploma or less
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- education level
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Spreadsheet
Description:
Abundance in Group 1: increased abundance in self-reported current cigarette smokers with high serum cotinine
NCBI | Links |
---|---|
Lactobacillus � | |
Scardovia � | |
Lactococcus � | |
Alloprevotella � | |
Campylobacter � | |
Porphyromonas � | |
Prevotella � | |
Anaeroglobus � | |
Veillonella � | |
Pseudomonas ⚠� | |
Fusobacterium � | |
Stomatobaculum � |
Revision editor(s): Kelvin Joseph