Thomas Sicheritz‐Pontén

The paper examines how different milk pretreatment methods affect microbiome dynamics during cheese production using metagenomic sequencing and identifies key microbial contributors to cheese quality.

The paper identifies Evangelion, a new family of anti-phage defence systems encoded in antimicrobial-resistance plasmids, through phenotype-guided analysis of a Staphylococcus aureus plasmid.

The paper compares INPHARED database snapshots from 2021 to 2026, showing growth in phage genomes but reduced novel species diversity and persistent host bias.

This study analyzes phage genomes to determine the frequency and mechanism of ARG acquisition, finding that ARGs are rarely present in phages and predominantly acquired via specialized transduction.

This study screens phage-antibiotic combinations in clinical isolates to identify synergistic interactions for treating resistant infections.

The paper identifies thousands of lytic phage genomes within bacterial assemblies, expanding known phage diversity and suggesting clinical isolates may contain therapeutic phage candidates.

TaxmyPHAGE automates the classification of dsDNA phage genomes into genera and species using MASH and BLASTn, enabling rapid and accurate taxonomic assignment at scale.

This study examines genomic plasticity in Salmonella lineages, revealing non-random integration of pathogenicity genes into regions of genomic plasticity and their regulatory relationships.

The paper sequenced the genome of an extinct Sardinian dhole to determine its evolutionary history and phylogenetic position, finding it diverged from Asian dholes and experienced gene flow before isolation.

The paper identifies and characterizes a novel receptor-binding protein from a Clostridium difficile phage, revealing its structure and function, and demonstrates the accuracy of AlphaFold2 predictions for structurome analysis.

This paper presents the first genome assembly and pangenome of Neonectria neomacrospora, revealing genetic diversity and functional features related to its plant pathogenic lifestyle.

The paper introduces a machine learning method for detecting prophages in bacterial genomes, finding more phages than existing tools while being faster.

This study uses whole-genome sequencing to analyze the population genetics of Neonectria neomacrospora, revealing clade divergence and gene flow patterns in Europe.

The paper analyzes the facial and gut microbiomes of vultures to identify microbial elements that contribute to their adaptation to scavenging diets.