The intestinal microbiota and human health are intimately linked, but interactions between bacteria and bacteriophages in the context of the mammalian intestine remain largely unexplored. We used comparative population genomics to study a tripartite network consisting of a virulent bacteriophage, its bacterial host, and a phage-insensitive bacterial strain both in vitro and within the murine gut. The bacteriophage adapted to infect the insensitive strain when the three partners co-existed in the gut of conventional mice, but not in dixenic mice or in planktonic cultures. The molecular changes associated with modifications in the bacteriophage host spectrum included single amino acid substitutions and an unusual homologous intragenomic recombination event within the genome of the bacteriophage. An intermediate bacterial host isolated from the murine microbiota mediated bacteriophage adaptation. Our data indicate that by offering access to new hosts, the microbiota shifts the genetic diversity of bacteriophages, thereby promoting long-term persistence of bacteriophage populations.

肠道菌群与人类健康有着密切的联系，但是在哺乳动物肠道中细菌与噬菌体之间的相互作用仍未得到充分探索。我们采用比较基因组学人口学三方网络由一个致命的噬菌体，其细菌宿主和噬菌体不敏感的细菌菌株都在体外并在鼠肠内。当三个伴侣共存于常规小鼠的肠道中，但不存在于二烯键小鼠或浮游培养物中时，噬菌体适于感染不敏感的菌株。与噬菌体宿主谱中的修饰相关的分子变化包括单个氨基酸取代和噬菌体基因组内的异常同源基因组重组事件。从鼠微生物群介导的中间细菌宿主介导的噬菌体适应。我们的数据表明，通过提供对新宿主的访问，微生物群改变了噬菌体的遗传多样性，从而促进了噬菌体种群的长期持久性。