Single Cell Genomics: Individual Faces in the Crowd

A paper by DCO collaborator Ramunas Stepanauskas discusses the rapidly improving technique of single cell genomics, including methodology and recent breakthroughs.

Single cell genomics (SCG) reveals hereditary information at the most basic level of biological organization. It is rapidly opening new scientific frontiers for the Deep Carbon Observatory as well as other research groups.

SCG is a powerful tool to identify metabolic features, evolutionary history, and inter-organismal interactions of the microbial groups that dominate many environments. It complements cultivation-based and microbial community-focused research approaches.

A paper by DCO collaborator Ramunas Stepanauskas discusses the rapidly improving technique, including methodology and recent breakthroughs. DNA sequencing was introduced to phylogenetic studies in the 1970s and applied to uncultured microorganisms in the 1980s and 1990s. The practice revolutionized microbiology and revealed that the immense diversity of unicellular life on Earth exceeded that discovered via classical cultivation techniques. Large metagenomics projects in the 2000s began providing extensive gene content information from natural microbial communities.

High-quality SCG results currently require expensive instrumentation, specialized infrastructure, and the concerted efforts of scientific personnel with a range of skills. These requirements mean that the technique is not available to most individual research groups. To address the challenge, Stepanauskas and colleagues established the Bigelow Laboratory Single Cell Genomics Center, the first user facility providing SCG services to the broad scientific community. The center has processed over 400,000 individual microbial cells sent by scientists from over 50 universities, research institutions, and companies. Another facility, the US Department of Energy Joint Genome Institute also offers services to external users. 

Stepanauskas recently expanded his DCO collaboration to work with the Deep Energy Community scientists in examining deep samples from the Kidd Creek Mine site in Ontario, Canada.

Figure:  The first user facility providing SGC services to the broad scientific community

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