Greg Caporaso, director of the Center for Applied Microbiome Science, part of the Pathogen and Microbiome Institute (PMI) at Northern Arizona University, has been awarded a $3.75 million grant by the National Cancer Institute (NCI) to build software capable of analyzing and archiving data focused on the interplay between the human microbiome (the trillions of microorganisms living in and on the human body) and diverse types of cancer.
“The development of certain types of cancer—gastric cancer and cervical cancer, for example—have well-established microbial links,” Caporaso said. “Our technologies for studying the human microbiome have rapidly advanced over the past two decades and continue to advance daily. As a result, we now have many new techniques to generate data on the composition and activities of the human microbiome, and many cancer researchers are working to use this information to understand new microbial links.
“However, since the analytic methods are so new, the software needed to turn this data into new knowledge is currently lacking. With this funding, we’ll fill that software gap with the development of new open source software for relating the human microbiome to cancer. We expect that will ultimately allow us to better understand cancer development, to detect cancer earlier and to improve cancer treatment and recovery.”
The NCI-funded project will enable Caporaso and his team to enhance QIIME 2, the bioinformatics software platform that they released in late 2016, to improve access to cancer microbiome bioinformatics methods and data. Caporaso’s team at NAU includes graduate and undergraduate students and full-time software engineers.
Matthew Dillon and Evan Bolyen, two research software engineers in Caporaso’s lab and co-first authors on the QIIME 2 paper, will be centrally involved in all of the design and development aspects of this project. The team plans to develop QIIME 2 into a microbiome multi-omics bioinformatics platform, supporting analysis and integration of genomic, metagenomic, metabolomics and other “-omics” data, driven by the needs of the cancer research community.
“Many important cancer microbiome projects have made advances by integrating different data types, yet considerable technical hurdles remain to making microbiome multi-omics bioinformatics accessible by all researchers whose projects would benefit from these methods,” Caporaso said.
With a background in software engineering, Caporaso’s previous project, QIIME 1, was started 12 years ago in collaboration with his post-doctorate adviser Rob Knight, now the director of the Center for Microbiome Innovation at the University of California, San Diego (UCSD). QIIME 1 was designed to facilitate their own studies into microbiomes—such as those found in humans or in soil—but also to make these methods accessible to all microbiome researchers.
Caporaso joined the faculty of NAU in 2011, where he continued his work on QIIME 1. Through his work with the Partnership for Native American Cancer Prevention, and subsequently during a sabbatical at the NCI, Caporaso realized the potential importance of the human microbiome to cancer. His primary papers on QIIME 1 and 2 have now been cited nearly 25,000 times in the primary research literature, making him one of the most highly cited researchers at NAU, according to Google Scholar, and Caporaso notes that nearly 20 percent of those citations are from studies about cancer. This led him to begin focusing efforts on better supporting the cancer research community with QIIME and ultimately to this five-year award from the NCI.
“This is exciting for cancer researchers because it’s going to enable a new type of study in microbiome research,” he said. “QIIME has typically been used to generate a taxonomic understanding of the microbiome—which microbes are present in this environment, and how communities of microbiomes compare to each other based on their taxonomic composition. New technologies are beginning to be applied to help us consider other factors, such as what biological activities the microbes are engaged in, and the metabolic products of those activities. Integrating these data, along with data about the host such as their genome, is sure to lead us to new mechanistic understandings of the role of the microbiome in cancer.”
QIIME 2 will support analysis of new types of data, such as metagenomics and metabolomics, to answer questions regarding the activity of microbes. This will include information on the functional genes encoded in microbial genomes and the metabolites present in the environment—small molecules like caffeine or ethanol and products produced by microbes—and how they might be impacting the host.
“With microbiome profiling, we’re getting an idea of the biology; with metabolite profiling, we’re getting a picture of the chemistry. That helps us understand the bigger, more holistic view of what’s going on in this infinitely complex environment of the gut microbiome where you’ve got trillions of cells interacting with each other and their environments, all creating and consuming metabolites, which impact their behavior and the behavior of our cells. We’ll be able to know not only who is there in terms of microorganisms, but what they are doing, where they are living and how they are interacting.”
As with QIIME 1, QIIME 2 is an open-source software platform, free and available for use by anyone. QIIME 2 was designed to expand automated methods of tracking and reporting to improve research reproducibility, and with this funding the team will create new tools to assist with long-term data archiving. Updates to QIIME 2 are released quarterly by Caporaso’s team, and they have already begun working toward some of the aims of this grant.
“This is an incredibly exciting project for the cancer microbiome research community,” said Melissa Herbst-Kralovetz, associate professor at the University of Arizona Cancer Center and director of the Women’s Health Research Program at The University of Arizona College of Medicine-Phoenix. “My lab investigates the role of microbiota in gynecologic cancer, sexually transmitted infections and women’s health. At present, we’re leveraging 3D in vitro human models to better understand the role of microbiota in cancer development and progression, which relies on integrating diverse data types from clinical samples and our lab-based 3D models. The new functionality being developed for QIIME 2 will help us to assess the accuracy of these models, and ultimately translate information we gain from these 3D models back to the clinic to fight cancer.”
“When we’re able to start connecting the host biology, the microbiology and the chemistry, that’s when we’re really going to be able to figure out some of the missing links between the microbiome and cancer development or cancer treatment,” Caporaso said.
Bonnie Stevens and Kerry Bennett | Office of the Vice President for Research