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.
Inoviruses are filamentous viruses with small, single-stranded DNA genomes and a unique chronic infection cycle. In Nature Microbiology, a team led by DOE Joint Genome Institute (JGI) researchers applied machine learning to publicly available microbial genomes and metagenomes to search for inoviruses. The search tool combed through more than 70,000 microbial and metagenome datasets, ultimately identifying more than 10,000 inovirus-like sequences compared to the 56 previously known inovirus genomes. The results revealed inoviruses are in every major microbial habitat—including soil, water, and humans—around the world.
“We’re not sure why we systematically manage to miss them; maybe it’s due to the way we currently isolate and extract viruses,” said the study’s lead author Simon Roux, a JGI research scientist in the Environmental Genomics group. Click here to read the full story on the JGI site.
In Nature, researchers in Berkeley Lab’s Biosciences Area, the Gladstone Institutes, and the Chan-Zuckerberg Biohub presented nearly 61,000 microbial genomes that were computationally reconstructed from 3,810 publicly available human gut metagenomes, which are datasets of all the genetic material present in a microbiome sample. The metagenome-assembled genomes (MAGs) included 2,058 previously unknown species, bringing the number of known human gut species to 4,558 and increasing the phylogenetic diversity of sequenced gut bacteria by 50 percent. This work helps answer the question of why certain microbes have not been cultivated in the lab. Read more in the Berkeley Lab News Center.