Bacterial antiviral immunity systems can be toxic to their hosts and must be tightly regulated. Immunity genes are often encoded by AT-rich mobile genetic elements subjected to silencing by nucleoid b...

Abstract. The KEGG Orthology (KO) system links DNA and protein sequences to biological functions and pathways, providing a curated, fundamental, and consis

Inside cells, DNA is intimately associated with proteins, forming chromatin. The protein constituents of chromatin vary across the tree of life: histones are the principal building blocks of chromatin...

Most of our knowledge about bacterial functional roles in microbiomes comes from bulk measurements. Yet microbial communities are complex ecosystems in which functionally distinct bacterial subpopulat...

Phage-bacteria interactions are typically studied in bulk culture, which obscures cell-cell differences. Here the authors study phage-bacteria interactions using single-cell transcriptomics, identifyi...

Pooled CRISPR screens using single-cell RNA sequencing (scRNA-seq) have emerged as powerful tools to uncover gene function, map regulatory networks, and identify genetic interactions. However, the inh...

An interface to compute pairwise ANI of NCBI genomes using the GTDB taxonomy.

Sponges are regarded among the earliest multicellular organisms and the most ancient examples of animal-bacterial symbiosis. The study of host-microbe interactions in sponges has advanced rapidly due ...

BrxX methylase in complex with SAM cofactor mediates foreign DNA recognition by the BREX system. BrxX can be engineered to modify BREX specificity and enhance defense. BREX defense and methylatio...

Marine sponges harbor diverse communities of associated organisms, including eukaryotes, viruses, and bacteria. Sponge associated microbiomes contribute to the health of the host organisms by defendin...

Success of phage therapies is limited by bacterial defenses against phages. While a large variety of anti-phage defense mechanisms has been characterized, how expression of these systems is distribute...