The ecological dynamics underlying the coexistence between antagonistic populations of bacteria and their viruses, bacteriophages (phages), in the mammalian gut microbiota remain poorly understood. We challenged a murine synthetic bacterial community with phages to study the factors allowing phages-bacteria coexistence. Coexistence was not dependent on the development of phage-resistant clones nor on the ability of phages to extend their host range. Instead, our data suggest that phage-inaccessible sites in the mucosa serve as a spatial refuge for bacteria. From there, bacteria disseminate in the gut lumen where they are predated by luminal phages fostering the presence of intestinal phage populations. The heterogeneous biogeography of microbes contributes to the long-term coexistence of phages with phage-susceptible bacteria. This observation could explain the persistence of intestinal phages in humans as well as the low efficiency of oral phage therapy against enteric pathogens in animal models and clinical trials.

在哺乳动物肠道菌群中，细菌与其病毒，噬菌体（噬菌体）的拮抗种群之间共存的生态动力学仍然知之甚少。我们用噬菌体挑战了鼠类合成细菌群落，以研究允许噬菌体与细菌共存的因素。共存既不依赖于噬菌体抗性克隆的发展，也不依赖于噬菌体扩展其宿主范围的能力。相反，我们的数据表明粘膜中噬菌体不可及的位点可作为细菌的空间庇护所。从那里，细菌在肠腔中传播，在那里它们被腔内噬菌体捕食，从而促进了肠道噬菌体种群的存在。微生物的异质生物地理学有助于噬菌体与噬菌体易感细菌的长期共存。