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This repo provides code to reproduce results from two published studies:

Beghini, F. et al. Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study. Ann. Epidemiol. 34, 18–25.e3 (2019)

Renson, A. et al. Sociodemographic variation in the oral microbiome. Ann. Epidemiol. 35, 73–80.e2 (2019)

Microbiome analysis of the NYC-HANES study

To reproduce this analysis, you need two packages from CRAN ( To install these from the R command line:

install.packages(c("BiocManager", "devtools"))

Then you can install this package and build its vignettes as follows:


On some machines, the above command may not by default install all the required dependencies. If this happens to you, you can install the nychanesmicrobiome package and its dependencies as follows:

BiocManager::install(c("waldronlab/nychanesmicrobiome", "phyloseq", "lsr", "sas7bdat", "kableExtra", 
          "ggplot2", "IHW", "dplyr", "epitools", "statmod", "DESeq2", "edgeR", "GSVA", 
          "EnrichmentBrowser", "magrittr", "dplyr", "vegan", "reshape2", "BiocStyle"))

After installing the nychanesmicrobiome package, load it by doing:


Then see the code and results of previous analyses by doing:


With the nychanesmicrobiome package loaded, you should be able to reproduce any of the code found in these "vignette" analyses. The nychanesmicrobiome package provides a number of documented functions for analysing this dataset. Some functions are defined in the package to keep the analysis scripts cleaner and separate out components used by multiple analysts:


In particular, loadQiimeData() will import the NYC HANES microbiome data as a phyloseq object, including cleaning and merging the participant data with the microbiome data.