Anil K Chaturvedi, Emily Vogtmann, Jianxin Shi, Yukiko Yano, Martin J Blaser, Nicholas A Bokulich, J Gregory Caporaso, Maura L Gillison, Barry I Graubard, Xing Hua, Autumn G Hullings, Lisa Kahle, Rob Knight, Shilan Li, Jody McLean, Vaishnavi Purandare, Yunhu Wan, Neal D Freedman, Christian C Abnet
{"title":"The mouth of America: the oral microbiome profile of the US population.","authors":"Anil K Chaturvedi, Emily Vogtmann, Jianxin Shi, Yukiko Yano, Martin J Blaser, Nicholas A Bokulich, J Gregory Caporaso, Maura L Gillison, Barry I Graubard, Xing Hua, Autumn G Hullings, Lisa Kahle, Rob Knight, Shilan Li, Jody McLean, Vaishnavi Purandare, Yunhu Wan, Neal D Freedman, Christian C Abnet","doi":"10.1101/2024.12.03.24318415","DOIUrl":null,"url":null,"abstract":"<p><strong>Importance: </strong>The oral microbiome is increasingly recognized to play key roles in human health and disease; yet, population-representative characterizations are lacking.</p><p><strong>Objective: </strong>Characterize the composition, diversity, and correlates of the oral microbiome among US adults.</p><p><strong>Design: </strong>Cross-sectional population-representative survey.</p><p><strong>Setting: </strong>The National Health and Nutrition Examination Survey (NHANES, 2009-2012), a stratified multistage probability sample of the US population.</p><p><strong>Participants: </strong>NHANES participants aged 18-69 years (n=8,237, representing 202,314,000 individuals).</p><p><strong>Exposures: </strong>Demographic, socioeconomic, behavioral, anthropometric, metabolic, and clinical characteristics.</p><p><strong>Main outcomes: </strong>Oral microbiome, characterized through 16S rRNA sequencing. Microbiome metrics were alpha diversity (number of observed Amplicon Sequence Variants [ASV], Faith's Phylogenetic diversity, Shannon-Weiner Index, and Simpson Index); beta diversity (unweighted UniFrac, weighted UniFrac, and Bray-Curtis dissimilarity); and prevalence and relative abundance at taxonomic levels (phylum through genus). Analyses accounted for the NHANES complex sample design.</p><p><strong>Results: </strong>Among US adults aged 18-69 years, the oral microbiome encompassed 37 bacterial phyla, 99 classes, 212 orders, 446 families, and 1,219 genera. Five phyla- <i>Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria,</i> and <i>Fusobacteria</i> and six genera- <i>Veillonella, Streptococcus, Prevotella7, Rothia, Actinomyces, and Gemella</i> , were present in nearly all US adults (weighted-prevalence >99%). These genera also were the most abundant, accounting for 65.7% of abundance. Observed ASVs showed a quadratic pattern with age (peak at 30 years), was similar by sex, significantly lower among non-Hispanic White individuals, and increased with higher body mass index (BMI) categories, alcohol use, and periodontal disease severity. All covariates together accounted for a modest proportion of oral microbiome variability, as measured by beta diversity (unweighted UniFrac=8.7%, weighted UniFrac=7.2%, and Bray-Curtis=6.3%). By contrast, relative abundance of a few genera explained a high percentage of variability in beta diversity (weighted UniFrac: <i>Aggregatibacter</i> =22.4%, <i>Lactococcus</i> =21.6%, <i>Haemophilus</i> =18.4%). Prevalence and relative abundance of numerous genera were significantly associated (Bonferroni-corrected Wald-p<0.0002) with age, race and ethnicity, smoking, BMI categories, alcohol use, and periodontal disease severity.</p><p><strong>Conclusions: </strong>We provide a contemporary reference standard for the oral microbiome of the US adult population. Our results indicate that a few genera were universally present in US adults and a different set of genera explained a high percentage of oral microbiome diversity across the population.</p>","PeriodicalId":94281,"journal":{"name":"medRxiv : the preprint server for health sciences","volume":" ","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11643230/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"medRxiv : the preprint server for health sciences","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1101/2024.12.03.24318415","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
Abstract
Importance: The oral microbiome is increasingly recognized to play key roles in human health and disease; yet, population-representative characterizations are lacking.
Objective: Characterize the composition, diversity, and correlates of the oral microbiome among US adults.
Setting: The National Health and Nutrition Examination Survey (NHANES, 2009-2012), a stratified multistage probability sample of the US population.
Participants: NHANES participants aged 18-69 years (n=8,237, representing 202,314,000 individuals).
Exposures: Demographic, socioeconomic, behavioral, anthropometric, metabolic, and clinical characteristics.
Main outcomes: Oral microbiome, characterized through 16S rRNA sequencing. Microbiome metrics were alpha diversity (number of observed Amplicon Sequence Variants [ASV], Faith's Phylogenetic diversity, Shannon-Weiner Index, and Simpson Index); beta diversity (unweighted UniFrac, weighted UniFrac, and Bray-Curtis dissimilarity); and prevalence and relative abundance at taxonomic levels (phylum through genus). Analyses accounted for the NHANES complex sample design.
Results: Among US adults aged 18-69 years, the oral microbiome encompassed 37 bacterial phyla, 99 classes, 212 orders, 446 families, and 1,219 genera. Five phyla- Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria, and Fusobacteria and six genera- Veillonella, Streptococcus, Prevotella7, Rothia, Actinomyces, and Gemella , were present in nearly all US adults (weighted-prevalence >99%). These genera also were the most abundant, accounting for 65.7% of abundance. Observed ASVs showed a quadratic pattern with age (peak at 30 years), was similar by sex, significantly lower among non-Hispanic White individuals, and increased with higher body mass index (BMI) categories, alcohol use, and periodontal disease severity. All covariates together accounted for a modest proportion of oral microbiome variability, as measured by beta diversity (unweighted UniFrac=8.7%, weighted UniFrac=7.2%, and Bray-Curtis=6.3%). By contrast, relative abundance of a few genera explained a high percentage of variability in beta diversity (weighted UniFrac: Aggregatibacter =22.4%, Lactococcus =21.6%, Haemophilus =18.4%). Prevalence and relative abundance of numerous genera were significantly associated (Bonferroni-corrected Wald-p<0.0002) with age, race and ethnicity, smoking, BMI categories, alcohol use, and periodontal disease severity.
Conclusions: We provide a contemporary reference standard for the oral microbiome of the US adult population. Our results indicate that a few genera were universally present in US adults and a different set of genera explained a high percentage of oral microbiome diversity across the population.