Research Microbiome analysis
We are working on ordination techniques and machine learning to link community dynamics to function. One of the first examples of using ordination and machine learning with 16S rRNA gene sequences was by our lab in a PNAS paper (free pdf of this paper) in collaboration with the Rob Knight Lab. My lab also collaborates with the Ruth Ley Lab at Cornell University (paper in Cell).
The Angenent Lab together with Jeff Werner have been using QIIME. Jeff Werner has developed an open-source software resource to install QIIME, which is called MacQIIME, and has also developed a teaching module with a detailed tutorial for you, so that you can get started to use QIIME. Besides a small dataset that is part of QIIME, Jeff has made available on his website our 454 pyrosequencing and metadata from nine full-scale anaerobic digesters. You can play with this dataset and compare your results with the beta diversity Figure in our above-mentioned PNAS paper (free pdf of this paper). Note that if you are using a windows or Linux machine, a Virtual Box is available to use QIIME.