The Micro-Scale Applications group explores the genetic makeup of natural microbial communities using a variety of cutting-edge approaches. For example, we operate a high throughput pipeline for sorting and amplifying the genomes of individual cells. Using this culture independent approach, we have performed whole genome amplification on 10,000’s of microbes collected from a diverse range of environments (e.g. hot springs, forest soils, subterranean aquifers, Antarctic lakes, plant roots, etc.), and recovered microbial genomes from uncultivated clades.
Our group also seeks out new approaches that utilize microfluidics/microdroplet technology in order to enhance the quality of single-cell genomes and directly link functional information with individual cells. We are particularly interested in new techniques that can assign functional activities to new groups of microbes or that can reveal links between uncultivated viruses and their microbial hosts.
Finally, we combine shotgun metagenomic sequencing with multi-year time series studies in order to follow changes in the genetic composition of natural microbial communities. In collaboration with Dr. Katherine McMahon at the University of Wisconsin, we have used this approach to assemble hundreds of population genomes, and we are now able to track the evolution of these populations over several years.
Research Team
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| Rex Malmstrom | Danielle Goudeau | W. Berkeley Kauffman |
| Read more about Rex. | Danielle operates the single-cell genomics pipeline for JGI collaborators. This work combines custom flow cytometric analysis, cell sorting, genome amplification, PCR screening, and 16S sequencing. She also develops novel flow cytometry protocols for targeted recovery of specific microbes. | Berkeley is responsible for receiving and processing user samples. His R&D work focuses on the development of new applications utilizing a variety of technologies to improve the JGI’s capabilities in the areas of metagenomics, single-particle genomics, and metabolic engineering. |
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| Nandita Nath | Kanwar Singh | Andy Tomatsu |
| Nandita is involved in developing new methods to improve genome recovery from single cells and to build sequencing libraries from minimal DNA input without amplification. | Kanwar spends part of his time assisting JGI users by processing their single cell samples using our high throughput pipeline. He also explores new methods for creating sequencing libraries and optimizing various processes. | Andy’s work focuses on the miniaturization and automation various molecular techniques using microfluidic devices. This includes DNA and RNA library creation from microbial cells captured using custom microfluidic chips, and single-cell transcriptomics of eukaryotes (e.g. Drop-seq). |