Article
Author: Sartor, Ryan Balfour ; Nicenboim, Julian ; Zelcbuch, Lior ; Sorek, Rotem ; Kern, Lara ; Lev, Vered ; Elinav, Eran ; Golembo, Myriam ; Furuichi, Munehiro ; Cohen, Ariel ; Harmelin, Alon ; Weinstock, Eyal ; Khabra, Efrat ; Zak, Naomi ; Kredo-Russo, Sharon ; Mohapatra, Gayatree ; Cuevas-Sierra, Amanda ; Bassan, Merav ; Inbar, Dana ; Stettner, Noa ; Weiner, Iddo Nadav ; Schramm, Christoph ; Maharshak, Nitsan ; Sokol, Harry ; Atarashi, Koji ; Kowalsman, Noga ; Honda, Kenya ; Lieb, Wolfgang ; Kario, Edith ; Geffen, Yael Friedman ; Dori-Bachash, Mally ; Federici, Sara ; Suez, Jotham ; Matiuhin, Yulia ; Cohen, Tal ; Moresi, Claudia ; Kviatcovsky, Denise ; Shapiro, Hagit ; Puttagunta, Sailaja ; Liu, Bo ; Gahali-Sass, Inbar ; Silberberg, Yael ; Bang, Corinna ; Ben-Yishai, Noa ; Franke, Andre ; Ben-David, Hava ; Oka, Akihiko ; Zheng, Danping ; Rappo, Urania ; Nobs, Samuel Philip ; Valdés-Mas, Rafael ; Cullin, Nyssa ; Fibelman, Morine
Human gut commensals are increasingly suggested to impact non-communicable diseases, such as inflammatory bowel diseases (IBD), yet their targeted suppression remains a daunting unmet challenge. In four geographically distinct IBD cohorts (n = 537), we identify a clade of Klebsiella pneumoniae (Kp) strains, featuring a unique antibiotics resistance and mobilome signature, to be strongly associated with disease exacerbation and severity. Transfer of clinical IBD-associated Kp strains into colitis-prone, germ-free, and colonized mice enhances intestinal inflammation. Stepwise generation of a lytic five-phage combination, targeting sensitive and resistant IBD-associated Kp clade members through distinct mechanisms, enables effective Kp suppression in colitis-prone mice, driving an attenuated inflammation and disease severity. Proof-of-concept assessment of Kp-targeting phages in an artificial human gut and in healthy volunteers demonstrates gastric acid-dependent phage resilience, safety, and viability in the lower gut. Collectively, we demonstrate the feasibility of orally administered combination phage therapy in avoiding resistance, while effectively inhibiting non-communicable disease-contributing pathobionts.