Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut
Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut
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DOI：
10.1073/pnas.1319470110
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发表时间：
2013-12-10
影响因子：
11.1
通讯作者：
Gordon, Jeffrey I.
中科院分区：
文献类型：
--
作者：
Reyes, Alejandro;Wu, Meng;Gordon, Jeffrey I.
细菌病毒（噬菌体）是地球上最丰富的生物群，并且比它们的细菌猎物/宿主具有更多的遗传多样性。为了表征它们作为塑造肠道微生物群落结构的因素的作用，成年无菌小鼠被 15 种已测序的人类细菌共生体定植，其中 13 种含有一种或多种预测的原噬菌体。其中一个成员是溶纤维拟杆菌 WH2，其代表的同基因转座子突变体文库覆盖了其 90% 的基因。一旦组装完毕，该群落就会遭受阶段性的噬菌体攻击，攻击对象是从五名健康人的粪便微生物群中纯化出来的活的或热灭活的病毒样颗粒（VLP）。对输入的混合 VLP 制剂中的 DNA 进行鸟枪测序，加上对肠道微生物群样本和来自无菌小鼠的纯化粪便 VLP 进行鸟枪测序，揭示了一种可重复的非同时攻击模式，持续超过 25 天，涉及 5 个噬菌体，这是之前没有描述过的。该系统使我们能够（i）将合并的VLP中存在的特定噬菌体的增加与特定细菌分类群的减少相关联，（ii）提供噬菌体抗性由于生态或表观遗传因素而发生的证据，（iii）追踪五个人类供体中五个噬菌体中每个噬菌体的起源以及受体小鼠之间和受体小鼠内的基因组变异程度，以及（iv）建立溶纤维芽孢杆菌原噬菌体内的基因座的显着体内适应性优势授予其宿主。总之，这些结果为肠道中噬菌体-细菌宿主动态提供了一个明确的社区范围的观点。
Bacterial viruses (phages) are the most abundant biological group on Earth and are more genetically diverse than their bacterial prey/hosts. To characterize their role as agents shaping gut microbial community structure, adult germ-free mice were colonized with a consortium of 15 sequenced human bacterial symbionts, 13 of which harbored one or more predicted prophages. One member, Bacteroides cellulosilyticus WH2, was represented by a library of isogenic transposon mutants that covered 90% of its genes. Once assembled, the community was subjected to a staged phage attack with a pool of live or heat-killed virus-like particles (VLPs) purified from the fecal microbiota of five healthy humans. Shotgun sequencing of DNA from the input pooled VLP preparation plus shotgun sequencing of gut microbiota samples and purified fecal VLPs from the gnotobiotic mice revealed a reproducible nonsimultaneous pattern of attack extending over a 25-d period that involved five phages, none described previously. This system allowed us to (i) correlate increases in specific phages present in the pooled VLPs with reductions in the representation of particular bacterial taxa, (ii) provide evidence that phage resistance occurred because of ecological or epigenetic factors, (iii) track the origin of each of the five phages among the five human donors plus the extent of their genome variation between and within recipient mice, and (iv) establish the dramatic in vivo fitness advantage that a locus within a B. cellulosilyticus prophage confers upon its host. Together, these results provide a defined community-wide view of phage-bacterial host dynamics in the gut.