JGI users studied microbial communities at hydrothermal vents and underwater volcanoes. They found a wealth of diversity in the microorganisms there, which could lead to the development of new biotechnologies around clean energy, biofuels and bioproducts.
In Cell Genomics, an international consortium led by researchers at the Joint Genome Institute team generated 824 new Actinobacteria genomes, which were were combined with nearly 5,000 publicly available ones and 1,100 metagenome-assembled genomes (MAGs) reconstructed from sequenced environmental samples in a previous study.
Biosciences Area staff recently hosted 40 PhD students from Wageningen University in the Netherlands over two days at Emery Station East (ESE) and the Integrative Genomics Building (IGB). The group launched their two-week California tour in the Bay Area, stopping by local biotechnology companies and prominent academic research institutions. The contingent visited ESE to tour the facility, make presentations, and discuss potential collaborations. At the IGB, the students attended a day-long symposium that included short talks, tours of several user facilities, and a poster reception.
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.
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.