CMI Researchers Receive Grant to Address Grand Challenges in Microbiome Science
San Diego, Calif., September 13, 2017 -- UC San Diego Center for Microbiome Innovation (CMI) researchers have been awarded $140,000 to address one of the grand challenges in microbiome science workflows – establishing standards for validating microbiome-focused workflows and enabling robust meta-analyses. The grant was awarded by CMI and was made possible in partnership with BASF, Biota, Illumina, Janssen and QIAGEN.
“Most of the research that has been done on the microbiome relies on relative measures – for example the abundance of an organism in a sample, relative to another – rather than absolute or quantitative values (i.e., the number of bacterial cells),” said Karsten Zengler, professor of pediatrics at UC San Diego and the recipient of the award.
Quantitative measurements are important for linking the metabolic activity of microbes to the physiological effects they have on the human body. “For example, if the concentration of a metabolite can be linked to the number of bacterial cells, a statement can be made about the absolute activity of this specific cell,” said Zengler.
Currently, it is possible to assess the absolute abundance of an organism, but it remains extremely challenging. Scientists are forced to use multiple time-consuming approaches, such as quantitative PCR, flow cytometry, species-specific fluorescence in situ hybridization, or a combination of single-cell and functional-targeting methods with genomics. Even though such methods exist, they are all currently limited to a few target genes or organisms and require prior knowledge of the types of organisms present in a sample.
Using the funds from the grant, Zengler aims to develop and initiate the commercialization of a universal method that enables the absolute abundance quantification of an organism, independent of sample origin and knowledge of the microbial community under investigation.
“This new method will enable the quantification of all sequence-based microbiome research,” said Zengler.
Zengler’s research is focused on using omics tools to understand how microbes interact with their partners, and the use of computational models to analyze and integrate the data.
The objective of the Center for Microbiome Innovation (CMI) is to accelerate microbiome research and understanding, through partnerships with industry sponsors. Together we will develop novel tools and methods to improve human health and benefit the environment by analyzing and manipulating microbiomes — the distinct and diverse communities of bacteria, viruses and other microorganisms that live within and around us. This is a multidisciplinary center with access to all the latest omics tools (genomics, metagenomics, metatranscriptomics, metabolomics, mutiplex proteomics), processing hundreds of thousands of samples each year and analyzing and collecting data for some of the largest microbiome cohorts in the world. Applications range from human disease understanding, ag bio, pharmaceutical, nutraceutical, environmental research, to consumer goods.
Center for Microbiome Innovation