This study identifies and characterizes prophage induction mechanisms in gut bacteria, showing that DNA damage reliably triggers induction of prophages encoding CI-like repressors.

bioRxiv · Jun 26, 2026 · PreprintMicrobiology

Mechanistic insights and clinical implications of cross-reactive anti-prophage antibodies and bacterial heteroresistance on phage therapeutic failure

Fernando L. Gordillo Altamirano, Dinesh Subedi, Mariel Beiers, Michael J Bucher, Sofia Dahlman, Devang M. Patel, M. Parker, Denis Korneev, Marcus J Robinson, Katherine Pragastis, J. Wisniewski, C. Rees, Hayley S. Ramshaw, Sadid F Khan, Bradley J. Gardiner, , Anton Yariv Peleg

The paper identifies pre-existing anti-prophage antibodies and bacterial heteroresistance as factors contributing to phage therapy failure in a patient with chronic infection.

Nature Medicine · Apr 24, 2026Peer-reviewedMicrobiology

Rational Design of Frontline Institutional Phage Cocktail for the Treatment of Nosocomial Enterobacter cloacae Complex Infections

Dinesh Subedi, Fernando L. Gordillo Altamirano, Rylee Deehan, Avindya Perera, Ruzeen Rohintan Patwa, Xenia Kostoulias, Denis Korneev, Luke V. Blakeway, Nenad Maćešić, Anton Yariv Peleg, Jeremy J. Barr

The paper develops a phage cocktail, Entelli-02, effective against multidrug-resistant Enterobacter cloacae complex strains with 99% coverage and 92% efficacy in a hospital strain collection.

Nature Microbiology · Sep 24, 2025Peer-reviewedMicrobiology

A novel CCDC112-dependent process of sperm midpiece formation and epididymal maturation

Maddison L. Graffeo, Joseph Nguyen, Farin Yazdan Parast, Donna Jo Merriner, Jessica E. M. Dunleavy, Denis Korneev, Hidenobu Okuda, Anne E. O’Connor, Donald F. Conrad, Reza Nosrati, Brendan J. Houston, Moira K. O’Bryan

This study identifies CCDC112 as essential for sperm mitochondrial sheath formation and epididymal maturation, impacting fertility and motility.

bioRxiv · Nov 5, 2024 · PreprintDevelopmental Biology

Oxygen plasma focused ion beam scanning electron microscopy for biological samples

Gorelick Sergey, Korneev Denis, Handley Ava, Gervinskas Gediminas, Oorschot Viola, Kaluza Owen L., Law Ruby H.P., Bryan Moira O’, Pocock Roger, Whisstock James C., de Marco Alex

This paper introduces oxygen plasma FIB-SEM as a faster and more versatile method for cellular tomography compared to gallium FIB-SEM.

bioRxiv · Oct 31, 2018 · PreprintCell Biology