The human microbiome has been the subject of increasing research, with scientists determined to unravel its role in a wide range of conditions including obesity, asthma, allergies, and inflammatory conditions of the gut. Because of the extensive diversity of the human body’s microbiome, as more and more research is conducted, there is an overflow of microbial sequence data in need of more systematic organization for more effective analyses.
Rob Knight, PhD, professor of pediatrics and computer science and engineering at the University of California, San Diego (UCSD), School of Medicine, has developed a solution to organize this large volume of data through a microbiome analysis platform named QIIME (pronounced “chime” and short for “Quantitative Insights Into Microbial Ecology”). This platform can be accessed internationally through BaseSpace, an app that uses cloud technology by San Diego-based Illumina, a company that specializes in developing tools for life sciences and genetic studies.
“Previously, we relied on personal contacts and scientific publications to spread the word about QIIME, and then users needed to download several different software packages to their own computers. Users also needed some technical programming skills to use QIIME,” explained Dr. Knight in a news release. “By working with Illumina, not only will many more researchers now be able to access QIIME from the cloud, the BaseSpace interface will make it much easier for non-technical researchers to analyze their data. This advancement will significantly ease the bottleneck in a variety of human and environmental microbiome studies.”
Today, QIIME is fully utilized by a pair of complex and highly sensitive microbiome investigations: the Human Microbiome Project, which was commissioned by the National Institutes of Health, and the American Gut Project, a crowd-sourced, crowd-funded initiative which currently has Dr. Knight and his team mass sequencing every conceivable human microbiome sample from any and all willing participants.
“QIIME has proven to be a widely successful open-source project — the original paper our group published on it in 2010 has been cited by more than three thousand other papers since,” said Yoshiki Vázquez-Baeza, an incoming UC San Diego Computer Science and Engineering graduate student in Dr. Knight’s lab. “This collaboration, among many other things, will help us expand our user base and increase the availability of our methods.” Like Dr. Knight and more than 25 other members of his lab, Vázquez-Baeza relocated from Colorado to UCSD this year, in part because of the collaborative spirit and innovative resources found in San Diego’s life sciences research and biotechnology community.
“BaseSpace is a cloud solution for data repository and analysis options that help streamline the processing of the seemingly ubiquitous genomic and metagenomic sequence data that researchers generate every day,” explained Jay Patel, associate product manager of BaseSpace applications at Illumina. “QIIME is a highly utilized tool in metagenomics research and we are excited to make it part of the Illumina ecosystem.”
“We look forward to using QIIME on BaseSpace for our upcoming deep dive into the differences in the human gut microbiome in healthy people compared to people with inflammatory bowel disease,” said Larry Smarr, PhD, professor and founding director of the California Institute for Telecommunications and Information Technology (Calit2) at UCSD.
In integrating research on the human microbiome in inflammatory bowel diseases (IBD), such as Crohn’s disease and ulcerative colitis, Drs. Knight and Smarr will rely on QIIME to help establish any microbes’ relationship with IBD. Their strategy involves the sequential analysis of stool samples from both IBD patients and healthy individuals through UCSD School of Medicine’s Institute for Genomic Medicine. Once sequencing of samples is completed, Drs. Knight and Smarr will be notified via email of their data’s availability on BaseSpace. Their team will simply have to log on to BaseSpace and access the QIIME app to view their study’s raw sequenced data before using the software to create a comparative 3-D scatterplot of the samples, to see the differences and similarities between the microbiome in IBD patients and healthy individuals. Any notable differences will cue Drs. Knight and Smarr to take the study deeper into the laboratory.
Prominent genomic and metagenomic assembly expert Pavel Pevzner, PhD, the Ronald R. Taylor Professor of Computer Science at UC San Diego and Howard Hughes Medical Institute, is pleased with the new software and believes its availability on BaseSpace is a milestone in the university and Illumina’s partnership in developing computational, life science tools.
“Our own software — SPAdes Genome Assembler — has been available in the Illumina BaseSpace app store for some time, and has helped thousands of users assemble their genome data in a range of medical and scientific applications,” said Dr. Pevzner, who also directs the NIH Center for Computational Mass Spectrometry. “Adding QIIME to the expanding toolbox of world-leading bioinformatics software for genomic and metagenomic analysis paves the way for future innovations and collaborations with Illumina in this space.”