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The Human Microbiome Biodiversity in Health and Disease

By Angela Peña-Gonzalez1, Emily Weigel1

Georgia Institute of Technology

The students will analyze the human gut and vaginal microbiomes in healthy and diseased states using diversity of bacteria as determined by 16SrRNA sequence.

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Version 1.0 - published on 17 Feb 2021 doi:10.25334/C094-BX29 - cite this

Licensed under CC Attribution-NoDerivatives 4.0 International according to these terms


Overview: High-throughput sequencing of PCR-amplified taxonomic markers like the 16S rRNA gene has enabled a new level of analysis of the human body’s complex microbial communities, which are collectively known as the human microbiome. Many tools exist to quantify and compare abundance levels of organisms via operational taxonomic units (OTUs) and to visualize the structure and composition of microbial communities in different conditions (e.g. healthy and diseased, or sick, states). In this introductory tutorial, we provide a simple workflow in R to perform basic analysis of gut and vaginal microbiome data in healthy and diseased states. This workflow is based on software packages from the open-source Bioconductor project ( and some CRAN packages.


Learning objectives:


1. Perform microbial ecology analysis of healthy and disease individuals based on the sequencing of the 16S rRNA gene.

2. Perform data analysis and visualization (barplots, boxplots, and dendrograms) using open source, statistical tools in R  

3. Test (non-parametric) statistical differences in community composition and structure within and between samples using computational tools.



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