10 Years Reading Life’s Blueprints, A Cell at a Time


Since its founding a decade ago, the Single Cell Genomics Center at Bigelow Laboratory has enabled discoveries in a huge range of fields – from the evolution of life to space exploration.

It was the first facility of its kind in the world, and its ever-expanding impact now spans multiple orders of magnitude: more than 100 published studies have utilized the Single Cell Genomics Center to analyze more than 1,000,000 individual cells to date.

"What we have achieved is the result of thousands of hours of hard work by dedicated staff, and constant innovation to perfect our processes," said Ramunas Stepanauskas, a senior research scientist and director of the center. "It’s been an exciting 10 years. I am proud of our accomplishments and excited about our future."

What became the Single Cell Genomics Center (SCGC) started small. When Stepanauskas came to Bigelow Laboratory in 2005, the field of single cell genomics didn’t yet exist. He and former-Senior Research Scientist Mike Sieracki were among the early explorers of the nascent field, tinkering with techniques to isolate single cells and achieve the incredible standards of cleanliness necessary to glean accurate data from them.

They became the first research team to successfully obtain completely clean DNA sequences from single cells. Next, they sought to expand their processing capacity, propelling it from just a few cells to thousands. Leveraging a grant from the National Science Foundation, they developed unparalleled infrastructure to support their efforts, and then established the Single Cell Genomics Center to extend these services to other researchers around the world.

At the time of its founding, SCGC was the first center for microbial single cell genomics. Today, it remains the largest center in the world to wield these complex and challenging techniques, and it is the only one to provide this revolutionary technology to any research group that seeks it. The unique capabilities of SCGC have illuminated processes in the deep sea, rewritten branches on the tree of life, and are even being used to help NASA reduce microbial contamination on the Mars rover set to launch in 2020.

"Interacting with so many collaborators has played a key role in stimulating this novel science and pushing the limits of our technology," Stepanauskas said. "The resulting approach has broad applications and the power to reveal things as diverse as potential anti-cancer drugs and insights into how the planet’s biosphere works."

Microbes are often tough to cultivate in the laboratory – and cultivation tends to bias which cells are detected. Single cell genomics enables researchers to analyze cells sampled straight from the environment, bypassing the cultivation step and avoiding the biases it can create.

In addition to offering this technology as a service to researchers worldwide, Stepanauskas and his team use it to power their own discoveries. They recently published research in Science that used single cell genomics to identify marine bacteria in the ocean depths that play a significant role in the global carbon cycle. Currently, Stepanauskas is leading a collaborative research team from Maine, New Hampshire and Nevada on a new, National Science Foundation-funded project. The team is developing new technologies to link the biological potential encoded in DNA with the actual processes performed by microorganisms in their natural environments.

Stepanauskas believes that some of SCGC’s most exciting work is yet to come. His team is working to create a comprehensive database of microbial genomes, building a foundation for molecular analyses that can aid a huge range of studies. They are also making progress toward addressing a fundamental challenge of microbiology – the definition of a species, which has always been unclear for bacteria and archaea.

"With the large amount of data that we're producing, we hope to resolve the boundaries between microbial lineages based on real patterns that emerge from the variation among genomes," Stepanauskas said. "What we’re learning is helping us develop new scientific theories and improve our understanding the vast numbers of microorganisms that inhabit every imaginable ecological niche on our planet."