Proksee: in-depth characterization and visualization of bacterial genomes

JR Grant, E Enns, E Marinier, A Mandal… - Nucleic acids …, 2023 - academic.oup.com
Abstract Proksee (https://proksee. ca) provides users with a powerful, easy-to-use, and
feature-rich system for assembling, annotating, analysing, and visualizing bacterial …

[HTML][HTML] Identification of mobile genetic elements with geNomad

AP Camargo, S Roux, F Schulz, M Babinski, Y Xu… - Nature …, 2023 - nature.com
Identifying and characterizing mobile genetic elements in sequencing data is essential for
understanding their diversity, ecology, biotechnological applications and impact on public …

[HTML][HTML] Prokaryotic Argonautes for in vivo biotechnology and molecular diagnostics

BA Graver, N Chakravarty, KV Solomon - Trends in Biotechnology, 2024 - cell.com
Prokaryotic Argonautes (pAgos) are an emerging class of programmable endonucleases
that are believed to be more flexible than existing CRISPR–Cas systems and have …

[HTML][HTML] Lachnospiraceae are emerging industrial biocatalysts and biotherapeutics

T Zaplana, S Miele, AC Tolonen - Frontiers in Bioengineering and …, 2024 - frontiersin.org
The Lachnospiraceae is a family of anaerobic bacteria in the class Clostridia with potential
to advance the bio-economy and intestinal therapeutics. Some species of Lachnospiraceae …

<? mode longmeta?> IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata

AP Camargo, L Call, S Roux, S Nayfach… - Nucleic acids …, 2024 - academic.oup.com
Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They
drive horizontal gene transfer, impacting ecological and evolutionary processes within …

Bacteria conjugate ubiquitin-like proteins to interfere with phage assembly

J Hör, SG Wolf, R Sorek - Nature, 2024 - nature.com
Several immune pathways in humans conjugate ubiquitin-like proteins to virus and host
molecules as a means of antiviral defence,,,–. Here we studied an antiphage defence …

The Vibrio cholerae CBASS phage defence system modulates resistance and killing by antifolate antibiotics

S Brenzinger, M Airoldi, AJ Ogunleye, K Jugovic… - Nature …, 2024 - nature.com
Toxic bacterial modules such as toxin–antitoxin systems hold antimicrobial potential, though
successful applications are rare. Here we show that in Vibrio cholerae the cyclic …

Sulfoquinovose is a widespread organosulfur substrate for Roseobacter clade bacteria in the ocean

L Liu, X Chen, J Ye, X Ma, Y Han, Y He… - The ISME …, 2023 - academic.oup.com
Sulfoquinovose (SQ) is one of the most abundant organosulfur compounds in the biosphere,
and its biosynthesis and degradation can represent an important contribution to the sulfur …

[HTML][HTML] Plant myo-inositol transport influences bacterial colonization phenotypes

BS O'Banion, P Jones, AA Demetros, BR Kelley… - Current Biology, 2023 - cell.com
Plant microbiomes are assembled and modified through a complex milieu of biotic and
abiotic factors. Despite dynamic and fluctuating contributing variables, specific host …

[HTML][HTML] Phylogenomics and genetic analysis of solvent-producing Clostridium species

RO Jensen, F Schulz, S Roux, DM Klingeman… - Scientific data, 2024 - nature.com
The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes),
whose members can encode useful complex traits such as solvent production, gas …