Interest in the microbiology of hydrocarbon-rich environments has increased  rapidly in recent years, with applications ranging from oil spill cleanup to reservoir management.

Modern techniques for reading out microbial communities using high-throughput sequencing produce vast amounts of data that cannot be processed by traditional methods.

Here, we describe the use of the QIIME pipeline for analyzing hydrocarbon-rich samples.

This pipeline starts with the raw data from high-throughput sequence analysis and produces graphical and statistical analyses suitable for publication or for decision support.

We illustrate the use of the QIIME pipeline using several recent datasets including sediments and water from the Deepwater Horizon spill and crude oil from a hydraulically fractured oil field in the United States, allowing better understanding of the microbiology of these systems.

QIIME is a free, open-source software and can be deployed on systems ranging from laptops to cloud computing environments.