Vibrant cities around the world are made up of a unique blend of cultures, languages, cuisines, and – as scientists recently revealed – microbes. Nearly 1,000 scientists from around the world, including three from Berkeley Lab, collected and analyzed microbial samples from public transit stations across 60 global cities. They probed ticket kiosks, benches, and rails to see what tiny organisms like bacteria, viruses, and archaea were in residence.
Solving a Genetic Mystery at the Heart of the COVID-19 Pandemic
As the COVID-19 pandemic enters its second year, scientists are still working to understand how the SARS-CoV-2 strain evolved, and how it became so much more dangerous than other coronaviruses, which humans have been living alongside for millennia. Virologists and epidemiologists worldwide have speculated for months that a protein called ORF8 likely holds the answer, and a recent study by Berkeley Lab scientists has helped confirm this hypothesis.
JGI’s CheckV Tool to Assess Virus Data Quality
Assembling viral genomes from metagenomes is challenging and often results in highly fragmented data, which limits the ability of researchers to accurately perform functional assessment, host prediction, and phylogenetic analysis. As reported in Nature Biotechnology, a team including JGI’s Stephen Nayfach, Frederik Schulz, Emiley Eloe-Fadrosh, Simon Roux and Nikos Kyrpides developed an automated tool called CheckV (pronounced “Check-Vee”) to help researchers assess and improve the quality of metagenome-assembled viral genomes. CheckV has already been applied to over 2.4 million viral genomes available in the latest release of IMG/VR, a database that is part of the Integrated Microbial Genomes & Microbiomes (IMG/M) suite. Learn more here on the JGI website.
JGI Team Describes Host-Virus Dynamics In a Microbial Mat
Previous work on microbial mats had primarily relied on culturing virus and host pairs in the laboratory to study their interactions. In The ISME Journal, a team co-led by JGI postdoctoral researcher Mária Džunková used single-cell sequencing to sequence both a cell’s genome and detect accompanying viral sequences, which would suggest the virus had been infecting the cell. Read the full story on the JGI website.
JGI Helps Conduct Antarctic Lake Time-Series Study
Through a decade-long time-series study recently reported in Microbiome, a team led by Rick Cavicchioli of Australia’s University of New South Wales and including JGI researchers found that light-harvesting bacteria in Antarctica’s Ace Lake defy the norm when it comes to nutrient cycling in polar regions. While microbial populations in other Antarctic lakes and the nearby Southern Ocean shift from phototrophs to archaea when sunlight becomes scant, Ace Lake’s bacteria instead go through a boom and bust cycle aligned with light availability. Read more on the JGI website.
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