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 Uniform resource identifier for web resources.
Authors
Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L, Dowd JB
Journal
Annals of epidemiology
Year
2019
PURPOSE: Variations in the oral microbiome are potentially implicated in social inequalities in oral disease, cancers, and metabolic disease. We describe sociodemographic variation of oral microbiomes in a diverse sample. METHODS: We performed 16S rRNA sequencing on mouthwash specimens in a subsample (n = 282) of the 2013-2014 population-based New York City Health and Nutrition Examination Study. We examined differential abundance of 216 operational taxonomic units, and alpha and beta diversity by age, sex, income, education, nativity, and race/ethnicity. For comparison, we examined differential abundance by diet, smoking status, and oral health behaviors. RESULTS: Sixty-nine operational taxonomic units were differentially abundant by any sociodemographic variable (false discovery rate < 0.01), including 27 by race/ethnicity, 21 by family income, 19 by education, 3 by sex. We found 49 differentially abundant by smoking status, 23 by diet, 12 by oral health behaviors. Genera differing for multiple sociodemographic characteristics included Lactobacillus, Prevotella, Porphyromonas, Fusobacterium. CONCLUSIONS: We identified oral microbiome variation consistent with health inequalities, more taxa differing by race/ethnicity than diet, and more by SES variables than oral health behaviors. Investigation is warranted into possible mediating effects of the oral microbiome in social disparities in oral and metabolic diseases and cancers.
Statistical test
edgeR
Experiment 1
Needs review
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
Needs review
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
Needs review
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
Needs review
Differences from previous experiment shown
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
Needs review
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
Needs review
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
Needs review
Differences from previous experiment shown
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
Needs review
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
Needs review
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
Needs review
Differences from previous experiment shown
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
Needs review
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
Retrieved from "https://bugsigdb.org/w/index.php?title=Study_635&oldid=108938"
Hidden category:
