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Microbiome Analyses of Oral Samples from the National Health and Nutrition Examination Survey (NHANES)

DCEG investigators are actively exploring the role of the human microbiome on risk for cancer. Critical to the success of such studies is the availability of high-quality, well-described participant data linked to biospecimens.

NHANES Oral Microbiome Data Resource

A new oral microbiome data source has been generated from samples collected from the National Health and Nutrition Examination Survey (NHANES). This is the first such nationally representative resource in the United States. Oral samples have been sequenced and paired with the robust phenotypic data from questionnaires and biometric measurements. Mortality data are available via linkage to the National Death Index.

Oral samples were collected from 2009-2012 to evaluate oral HPV prevalence among individuals in NHANES ranging in age from 14-69 years old. The DNA from these oral samples was then used for microbiome sequencing. The project is described in Vogtmann E et al. Representative oral microbiome data for the US population: the National Health and Nutrition Examination Survey. Lancet Microbe 2022. 

Data Availability

The alpha and beta diversity data are available on the NHANES website (posted October 2022).  

Raw sequencing files, ASV tables, relative abundance, and read count data for the phylum to genus levels are available for analysis through a proposal request to the National Center for Health Statistics Research Data Center (RDC).

Quality control data generated in this project from artificial communities, chemostat communities, and blanks are available on SRA [PRJNA896165].

For more information, contact Christian Abnet.

Metabolic Epidemiology Branch - Research Areas

This project was supported by DCEG and the US Food and Drug Administration’s Center for Tobacco Products.

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