Software, microbiome research, and bioinformatics education.


QIIME 2 is an open source, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results. QIIME 2 is the successor to QIIME 1 and has been completely redesigned and rewritten from the ground up.
scikit-bio is an open-source, BSD-licensed Python package providing data structures, algorithms, and educational resources for bioinformatics.
QIIME 1 is an open-source, GPL-licensed platform for the analysis and comparison of microbial communities (or microbiomes) based on DNA sequence data. QIIME 1 is very widely used, having been cited over 16000 times since its publication in 2010. NOTE: QIIME 2 has succeeded QIIME 1 as of January 1, 2018. QIIME 1 is no longer supported at this time.
Keemei is an open-source Google Sheets add-on for validating bioinformatics metadata, including QIIME mapping files.
cual-id is an open-source, BSD-licensed Python package for creating and managing unique, correctable sample identifiers and barcodes for use in any project containing multiple samples.

Representative microbiome projects

Longitudinal and spatial characterization of microbial communities in offices
As North Americans we spend the vast majority of our time indoors. We know that microbial communities cohabit our indoor spaces, including our homes and offices, but we know very little about what factors drive effect the microbial communities that establish in these environments. This study investigates the effect of climate and building parameters on how and what microbes establish in office buildings.
Moisture, wetting, and fungal growth measurement on common indoor surfaces.
This project aims to characterize, both qualitatively and quantitiatively, the fungal communities that establish on drywall surfaces when they're exposed to moisture. We'll simulate different sources of water infiltration in built environments, such as flooding and leaks, and characterize fungal communities on drywall in real environments that have been damaged by moisture.
The human gut microbiota and its viruses - Keys to treating autism?
Recent studies suggest that gut microbiota have a role in Autism Spectrum Disorders (ASD), potentially arising from their role in modulating the immune system and gastrointestinal (GI) function. We are examining changes in behavior, GI symptoms and the gut microbial and viral communities before and after administration of the FMT treatment over 18 weeks.
Microbes, bile acids and colorectal cancer
In this study we're testing a mechanistic hypothesis about how treatment of colorectal adenoma and cancer (CRA and CRC) patients with Ursodeoxycholic acid (UDCA) reduces the recurrance of CRA by profiling gut microbial communities and bile acids before and after treatment with UDCA.
Exercise Microbiome Project (EXMP)
The aim of this research project is to track changes in the human gut microbiome (the trillions of microorganisms living in the human gut) that happen when you perform physical activity.The research team will study the link between changes in physical activity and the gut microbiome and will provide initial data for investigation into the possible causes of change to the healthy human gut microbiome over time.

Bioinformatics education

A free, open source interactive text that introduces readers to core concepts of bioinformatics in the context of their implementation and application.
Dr. Caporaso's Northern Arizona University bioinformatics teaching website. This site contains all of Dr. Caporaso's teaching materials as well as information on current, past and future bioinformatics course offerings at NAU.
We regularly teach QIIME workshops at conferences and universities around the world. These are hands-on, and work best when they're designed to be 2-3 days for approximately 30 students.
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