Genomes OnLine Database (GOLD) v. 8: overview and updates

S Mukherjee, D Stamatis, J Bertsch… - Nucleic acids …, 2021 - academic.oup.com
Abstract The Genomes OnLine Database (GOLD)(https://gold. jgi. doe. gov/) is a manually
curated, daily updated collection of genome projects and their metadata accumulated from …

Prokaryotic taxonomy and nomenclature in the age of big sequence data

P Hugenholtz, M Chuvochina, A Oren… - the ISME …, 2021 - academic.oup.com
The classification of life forms into a hierarchical system (taxonomy) and the application of
names to this hierarchy (nomenclature) is at a turning point in microbiology. The …

[HTML][HTML] An expanded arsenal of immune systems that protect bacteria from phages

A Millman, S Melamed, A Leavitt, S Doron… - Cell host & …, 2022 - cell.com
Bacterial anti-phage systems are frequently clustered in microbial genomes, forming
defense islands. This property enabled the recent discovery of multiple defense systems …

The IMG/M data management and analysis system v. 7: content updates and new features

IMA Chen, K Chu, K Palaniappan, A Ratner… - Nucleic acids …, 2023 - academic.oup.com
Abstract The Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img. jgi.
doe. gov/m/) at the Department of Energy (DOE) Joint Genome Institute (JGI) continues to …

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

A Heinken, J Hertel, G Acharya, DA Ravcheev… - Nature …, 2023 - nature.com
The human microbiome influences the efficacy and safety of a wide variety of commonly
prescribed drugs. Designing precision medicine approaches that incorporate microbial …

[HTML][HTML] Phages and their satellites encode hotspots of antiviral systems

F Rousset, F Depardieu, S Miele, J Dowding… - Cell host & …, 2022 - cell.com
Bacteria carry diverse genetic systems to defend against viral infection, some of which are
found within prophages where they inhibit competing viruses. Phage satellites pose …

A genomic catalog of Earth's microbiomes

S Nayfach, S Roux, R Seshadri, D Udwary… - Nature …, 2021 - nature.com
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has
enabled insights into the ecology and evolution of environmental and host-associated …

Sourcing thermotolerant poly (ethylene terephthalate) hydrolase scaffolds from natural diversity

E Erickson, JE Gado, L Avilán, F Bratti… - Nature …, 2022 - nature.com
Enzymatic deconstruction of poly (ethylene terephthalate)(PET) is under intense
investigation, given the ability of hydrolase enzymes to depolymerize PET to its constituent …

A unified catalog of 204,938 reference genomes from the human gut microbiome

A Almeida, S Nayfach, M Boland, F Strozzi… - Nature …, 2021 - nature.com
Comprehensive, high-quality reference genomes are required for functional characterization
and taxonomic assignment of the human gut microbiota. We present the Unified Human …

DRAM for distilling microbial metabolism to automate the curation of microbiome function

M Shaffer, MA Borton, BB McGivern… - Nucleic acids …, 2020 - academic.oup.com
Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the
specific reactions catalyzed by these biological engines are hard to decode due to the …