Defining the human gut host-phage network through single-cell viral tagging
Defining the human gut host-phage network through single-cell viral tagging
复制标题
DOI：
10.1038/s41564-019-0526-2
复制
发表时间：
2019-12-01
影响因子：
28.3
通讯作者：
Hugenholtz, Philip
中科院分区：
文献类型：
--
作者：
Dzunkova, Maria;Low, Soo Jen;Hugenholtz, Philip
由于不依赖于培养的基于序列的分析的持续进步，病毒发现正以前所未有的速度加速。这一发现的一个重要方面是鉴定这些最近表征的未培养病毒的宿主。为此，我们采用了病毒标记方法，该方法绕过了对基于培养的方法来鉴定宿主-噬菌体配对的需要。标记的匿名病毒体吸附到未标记的匿名细菌宿主细胞上，然后将其单独分选为宿主-噬菌体对，然后进行基因组扩增和高通量测序，以确定宿主和附着病毒的身份。我们展示了使用粪便微生物组的单细胞病毒标记，包括人类受试者之间的病毒和细菌的交叉标记。预测了总共363种独特的宿主-噬菌体配对，其中大多数是受试者特异性的，并且涉及以前未表征的病毒，尽管它们的大多数细菌宿主具有已知的分类。这些对中的五分之一被多个单独的标记细胞确认。在宿主-噬菌体网络中明显不存在针对一个以上细菌物种的病毒，这表明噬菌体不是人类肠道中物种间水平基因转移的主要载体。尽管存在受试者特异性病毒谱，但注意到粪便和来自不同受试者的细菌之间的高水平交叉反应性，这对粪便微生物群移植治疗有影响。
Viral discovery is accelerating at an unprecedented rate due to continuing advances in culture-independent sequence-based analyses. One important facet of this discovery is identification of the hosts of these recently characterized uncultured viruses. To this end, we have adapted the viral tagging approach, which bypasses the need for culture-based methods to identify host-phage pairings. Fluorescently labelled anonymous virions adsorb to unlabelled anonymous bacterial host cells, which are then individually sorted as host-phage pairs, followed by genome amplification and high-throughput sequencing to establish the identities of both the host and the attached virus(es). We demonstrate single-cell viral tagging using the faecal microbiome, including cross-tagging of viruses and bacteria between human subjects. A total of 363 unique host-phage pairings were predicted, most of which were subject-specific and involved previously uncharacterized viruses despite the majority of their bacterial hosts having known taxonomy. One-fifth of these pairs were confirmed by multiple individual tagged cells. Viruses targeting more than one bacterial species were conspicuously absent in the host-phage network, suggesting that phages are not major vectors of inter-species horizontal gene transfer in the human gut. A high level of cross-reactivity between phages and bacteria from different subjects was noted despite subject-specific viral profiles, which has implications for faecal micro-biota transplant therapy.