1. Metataxonomics

Metataxonomics allows us to investigate the composition of a microbial community using amplicons from a targeted marker gene in order to make taxonomic inferences. A variety of tools and analysis pipelines have been developed to deal with this type of data. Some of the most popular ones are QIIME and Mothur.

QIIME provides a set of integratable scripts for analyzing raw microbial DNA samples including taxonomic classification using marker genes such as 16S rRNA, but allowing flexible pipelines to be constructed. Although Mothur was initially designed to target the microbial ecology community, it has since been adopted by the human microbiome community as well. It provides an extensible package with functionality accessible through a domain-specific language. Like QIIME, Mothur is also a metataxonomic tool, focusing on marker genes such as 16S rRNA.

1.1 16S

General tutorials

• Using QIIME to analyze 16S rRNA gene sequences from Microbial Communities
• Large-scale data analysis using subsampled open-reference clustering (QIIME)

Illumina

• Official Mothur MiSeq SOP
• Mealybugs’s metagenomic pipeline using Mothur
• Illumina Overview Tutorial using QIIME: Moving Pictures of the Human Microbiome

454

• Official Mothur 454 SOP
• 454 Overview Tutorial using QIIME: de novo OTU picking and diversity analyses using 454 data

1.2 18S

• Analysis of 18S data using QIIME

1.3 ITS

• Fungal ITS QIIME analysis tutorial