Computer code co-developed by a scientist from Lawrence Berkeley National Laboratory (Berkeley Lab) and embraced by the global science community over two decades has been hailed by Nature as one of “ten computer codes that transformed science.”
Microorganisms play key roles in regulating global nutrient cycles but only a small fraction has been identified and an even smaller number has been successfully cultured in a lab for study. In Nature Biotechnology, the known diversity of bacteria and archaea has now expanded by 44% through a publicly available collection of more than 52,000 microbial genomes from environmental samples. Of that number, 70% of the novel genome sequences were previously unknown, not yet cultured in the lab. The work results from a JGI-led collaboration involving more than 200 scientists around the world, KBase and NERSC. Read more about the genomic catalog of Earth’s microbiomes on the JGI website.
Biosciences Area researchers have developed a new DNA analysis technique that reveals a very interesting, and previously hard-to-study, aspect of a microbial community’s genome. As described in the journal mBio, a team led by Aindrila Mukhopadhyay of the Biological Systems and Engineering (BSE) Division has optimized existing methods to isolate plasmids—the small packages of DNA that enable microorganisms like bacteria to quickly acquire and share genes. Often, these DNA molecules, which are separate from the chromosomes, encode functions that can confer a survival advantage in certain situations. The work was conducted as part of ENIGMA, in collaboration with groups at Oak Ridge Field Research Center and the DOE Systems Biology Knowledgebase (KBase). Read the press release in the Berkeley Lab News Center.
Two teams of Biosciences Area researchers are representing Berkeley Lab as part of cohort eight of the U.S. Department of Energy’s I-Corps program, an intensive two-month training course that pairs national laboratory researchers with industry mentors to develop viable market pathways for their technologies. The teams, led by Deepti Tanjore and Esther Singer, presented their projects during the opening session held October 1–5 in Golden, Colorado.
In a letter to the editor published July 6 in Nature Biotechnology, the KBase team presented a comprehensive overview of the platform and an assessment of its scientific impact. The paper describes the unique features and infrastructure of the platform, in addition to highlighting scientific use cases that demonstrate its significance for biology research.