Sarah Vreugde

The paper re-speciates Corynebacterium using genome data from 87 isolates and identifies four novel species candidates, resolving taxonomic conflicts and clarifying functional roles.

The paper identifies mutations in the mfd gene in S. aureus isolates from a CRS patient, linking them to a mucoid hyper-biofilm phenotype and increased enterotoxin production.

Baktfold improves protein functional annotation for microbial genomes using structural information, achieving higher annotation rates than existing tools for bacteria and archaea.

Phold pairs ProstT5-predicted 3Di tokens with Foldseek searches against 1,363,704 curated phage structures, annotating 49.4% of CDS in 1,419 INPHARED genomes versus 34.7% for Pharokka MMseqs2.

The paper identifies three novel phages targeting vancomycin-resistant E. faecalis and shows that LicD-mediated cell wall decoration influences phage sensitivity and biofilm formation.

Roughly 25× short-read depth polishes nearly all residual errors in Nanopore-only bacterial assemblies; new '--careful' modes in Pypolca and Polypolish largely avoid introducing low-depth errors.

Hybracter improves bacterial genome assembly accuracy and speed, outperforming existing tools in hybrid and long-read-only modes, especially for small plasmids.

This study compares full-length 16S rRNA sequencing using Oxford Nanopore Technology (FL-ONT) with Illumina V3-V4 short-read sequencing in head and neck cancer tissues, finding FL-ONT provides better resolution at lower taxonomic levels.