The human gut is a complex environment that contains a multitude of microorganisms that are collectively termed the microbiome. Multiple factors have a role to play in driving the composition of human gut bacterial communities either toward homeostasis or the instability that is associated with many disease states. One of the most important forces are likely to be bacteriophages, bacteria-infecting viruses that constitute by far the largest portion of the human gut virome. Despite this, bacteriophages (phages) are the one of the least studied residents of the gut. This is largely due to the challenges associated with studying these difficult to culture entities. Modern high throughput sequencing technologies have played an important role in improving our understanding of the human gut phageome but much of the generated sequencing data remains uncharacterised. Overcoming this requires database-independent bioinformatic pipelines and even those phages that are successfully characterized only provide limited insight into their associated biological properties, and thus most viral sequences have been characterized as “viral dark matter.” Fundamental to understanding the role of phages in shaping the human gut microbiome, and in turn perhaps influencing human health, is how they interact with their bacterial hosts. An essential aspect is the isolation of novel phage-bacteria host pairs by direct isolation through various screening methods, which can transform in silico phages into a biological reality. However, this is also beset with multiple challenges including culturing difficulties and the use of traditional methods, such as plaquing, which may bias which phage-host pairs that can be successfully isolated. Phage-bacteria interactions may be influenced by many aspects of complex human gut biology which can be difficult to reproduce under laboratory conditions. Here we discuss some of the main findings associated with the human gut phageome to date including composition, our understanding of phage-host interactions, particularly the observed persistence of virulent phages and their hosts, as well as factors that may influence these highly intricate relationships. We also discuss current methodologies and bottlenecks hindering progression in this field and identify potential steps that may be useful in overcoming these hurdles.

人的肠道是一个复杂的环境，其中包含多种微生物，这些微生物统称为微生物组。多种因素在推动人类肠道细菌群落组成向稳态或与许多疾病状态相关的不稳定性方面发挥作用。最重要的力量之一可能是噬菌体，它们是感染人类肠道病毒的最大部分的细菌感染病毒。尽管如此，噬菌体（噬菌体）是肠道中研究最少的居民之一。这主要是由于与研究这些难以培养的实体相关的挑战。现代高通量测序技术在增进我们对人类肠道噬菌体的了解方面发挥了重要作用，但是生成的许多测序数据仍未表征。克服这一点需要独立于数据库的生物信息流水线，即使成功表征的噬菌体也只能对其相关的生物学特性提供有限的见识，因此大多数病毒序列已被表征为“病毒暗物质”。噬菌体如何与细菌宿主相互作用是理解噬菌体在塑造人类肠道微生物组中的作用的基础，而反过来又可能影响人类健康。一个重要方面是通过各种筛选方法直接分离来分离新的噬菌体-细菌宿主对，这可以转化为 克服这一点需要独立于数据库的生物信息流水线，即使成功表征的噬菌体也只能对其相关的生物学特性提供有限的见识，因此大多数病毒序列已被表征为“病毒暗物质”。噬菌体如何与细菌宿主相互作用是理解噬菌体在塑造人类肠道微生物组中的作用的基础，而反过来又可能影响人类健康。一个重要方面是通过各种筛选方法直接分离来分离新的噬菌体-细菌宿主对，这可以转化为 克服这一点需要独立于数据库的生物信息流水线，即使成功表征的噬菌体也只能对其相关的生物学特性提供有限的见识，因此大多数病毒序列已被表征为“病毒暗物质”。噬菌体如何与细菌宿主相互作用是理解噬菌体在塑造人类肠道微生物组中的作用的基础，而反过来又可能影响人类健康。一个重要方面是通过各种筛选方法直接分离来分离新的噬菌体-细菌宿主对，这可以转化为 它们如何与细菌宿主相互作用，是了解噬菌体在塑造人类肠道微生物组中的作用的基础，进而可能影响人类健康。一个重要方面是通过各种筛选方法直接分离来分离新的噬菌体-细菌宿主对，这可以转化为 它们如何与细菌宿主相互作用，是了解噬菌体在塑造人类肠道微生物组中的作用的基础，进而可能影响人类健康。一个重要方面是通过各种筛选方法直接分离来分离新的噬菌体-细菌宿主对，这可以转化为在计算机上噬菌体进入生物现实。然而，这也受到多重挑战的困扰，包括培养困难和使用诸如噬菌斑的传统方法，这可能偏向于哪些噬菌体-宿主对可以成功分离。噬菌体与细菌的相互作用可能受到复杂的人体肠道生物学的许多方面的影响，而这些方面在实验室条件下可能难以复制。在这里，我们讨论了迄今为止与人类肠道噬菌体相关的一些主要发现，包括组成，我们对噬菌体-宿主相互作用的理解，特别是观察到的有毒噬菌体及其宿主的持久性，以及可能影响这些高度复杂关系的因素。