James A D Docherty

The paper introduces PHORAGER, a pipeline for identifying prophages in bacterial genomes, and reports the discovery of 23,132 putative prophages in ESKAPE pathogens.

This study profiles the infant gut virome using dual methods and finds associations with eczema and wheeze.

This study examines the impact of a bacteriophage cocktail on healthy gut microbiota using an in vitro human colon model, finding minimal disruption with specific effects on Escherichia coli.

The paper identifies and analyzes prophages in infant-derived Bifidobacterium longum subspecies, revealing their antagonistic and synergistic strategies for persistence in the gut.

This study analyzes prophages and defense systems in Bifidobacterium genomes to reveal co-evolutionary 'arms race' dynamics between bacteria and phages.

The paper identifies a novel subspecies of Bifidobacterium longum, BL. nexti, in infant gut microbiomes, showing its association with formula feeding and vertical transmission.