Sociodemographic variation in the oral microbiome

From BugSigDB
Needs review
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.

Experiment 1


Needs review

Curated date: 2023/04/12

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph, Claregrieve1

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
Statistical test
edgeR
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

Curated date: 2023/04/13

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph

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

NCBI Links
uncultured bacterium
Neisseria
Bergeyella
Haemophilus
Lactococcus
Lautropia
Porphyromonas
Gemella
Streptobacillus
Fusobacterium
Bifidobacterium
Alloprevotella
Cardiobacterium
Capnocytophaga
Prevotella

Revision editor(s): Kelvin Joseph

Signature 2

Needs review

Curated date: 2023/04/15

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph

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

NCBI Links
Veillonella
Pseudomonas
Campylobacter
Leptotrichia
Anaeroglobus
Lactobacillus
Megasphaera
Alloscardovia
Alloprevotella
Streptococcus
Rothia
Stomatobaculum
Prevotella
Actinomyces

Revision editor(s): Kelvin Joseph

Experiment 2


Needs review

Curated date: 2023/04/24

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph

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

Curated date: 2023/05/01

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph

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

Curated date: 2023/05/02

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph

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

Curated date: 2023/05/02

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph

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

Curated date: 2023/05/02

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph

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

Curated date: 2023/05/02

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph

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

NCBI Links
Alloprevotella
Atopobium
Catonella
Dialister
Filifactor
Fusobacterium
Lactobacillus
Leptotrichia
Peptostreptococcus
Porphyromonas
Prevotella
Pseudomonas
Streptobacillus
Treponema
Veillonella
uncultured bacterium

Revision editor(s): Kelvin Joseph

Experiment 4


Needs review

Curated date: 2023/05/02

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph

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

Curated date: 2023/05/02

Curator: Kelvin Joseph

Revision editor(s): Kelvin Joseph

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