Case study using the Human Microbiome Project's data

This tutorial is aimed at showing researchers how to conduct different comparative metagenomic analyses. We compared microbial communities of 20 individuals obtained from the HMP. We downloaded 16S V3-V5 and shotgun pre-processed data from 10 buccal mucosa (BM) samples and 10 tongue dorsum (TD) samples using the HMP's data access browser.

The methods shown here were used in the book chapter:

Comparative Metagenomics, part of Comparative Genomics, Methods in Molecular Biology edited by Setubal, Stadler, Stoye. 2017.

Contributors:

• Andrew Maltez Thomas -> andrewmaltezthomas@gmail.com

• Felipe Prata Silva -> felipepratalima@gmail.com

• Livia Moura -> liviam.moura@gmail.com

System Requirements:

• Qiime (version < 2.0)
• R + R packages: vegan, phyloseq, ggplot2, plyr, reshape2, tidyr, curl, gplots, xlsx
• Biom
• LEfSe

Analyses:

Pre-processing the data

Analysis for Figure 1

Analysis for Figure 2

Analysis for Figure 3

Analysis for Figure 4

Analysis for Figure 5