2. Phage Distribution in the Human Body
2.噬菌体在人体内的分布
2.1. Composition of the Gut Phageome
2.1.肠道噬菌体的组成
The intestinal microbiota has been shown to play a major role in physiological processes in host organisms and its dysregulation has been linked to the development of many diseases, such as irritable bowel syndrome (IBS), colorectal cancer, obesity, inflammatory bowel disease (IBD), Clostridium difficile infection, or neurological disorders [37,38,39,40,41]. The bacterial community, which is a primary component, plays a crucial role in mammalian gut physiology. It facilitates metabolic functions, protects against pathogens, and modulates the immune response [7,8,42]. The human gut is also a place where fungi and viruses—especially bacteriophages—are observed [19,23,24,25]. Their role is to shape the structure of the bacterial community by specific lysis (disintegration or decomposition of the cell wall structure) of particular bacteria, but also by modulating the activity of the immune system, mediating the anti-inflammatory response, as well as playing a protective role against invasion of pathogens [14,16,43,44].
肠道微生物群在宿主生物的生理过程中发挥着重要作用，其失调与许多疾病的发生有关，如肠易激综合征（IBS）、结肠直肠癌、肥胖症、炎症性肠病（IBD）、艰难梭菌感染或神经系统疾病[37, 38, 39, 40, 41]。细菌群落作为主要组成部分，在哺乳动物肠道生理中发挥着至关重要的作用。它促进新陈代谢功能，抵御病原体，调节免疫反应[7, 8, 42]。人类肠道也是真菌和病毒（尤其是噬菌体）的聚集地 [ 19, 23, 24, 25]。噬菌体的作用是通过特定细菌的特定裂解（细胞壁结构的瓦解或分解）来塑造细菌群落的结构，同时还能调节免疫系统的活动，介导抗炎反应，并在病原体入侵时发挥保护作用[14、16、43、44]。
Bacteriophages follow one of two main life cycles: lytic and lysogenic. In the lytic cycle, the complete destruction of bacterial cells is observed. These bacteriophages (lytic, virulent) use host cell machinery to replicate and assemble new phage virions. On the other hand, the lysogenic cycle is favored by temperate phages, which base their life cycles on the ability to integrate their genetic material with the host genome and switch to the latent stage in the form of so-called prophages. Such phages can also enter the lytic cycle in response to certain conditions, lyse the cell, and release progeny virions into the environment. It is reported that the lysogenic cycle is favored by phages inhabiting human and animal bodies [45,46]. By comparison, bacteriophages in aquatic ecosystems prefer the classic “kill-the-winner” dynamic [46,47]. The reason for this is still unclear, but Knowles et al. hypothesized that the polarity between the ecosystem of the human body and aquatic ecosystems is based on the observation that temperate phages become increasingly important in diverse ecosystems, especially those of high microbial densities [48]. These phages can modulate gene expression in bacteria and alter their phenotype through transposition, induction, and horizontal gene transfer (HGT). Temperate phages may also transfer virulence or antibiotic-resistance genes between bacterial cells. The vast repertoire of genes can shape bacterial diversity and function; thus, bacteriophages contribute to bacterial balance and homeostasis. Shifts in the composition of the virome (mainly phageome) affect human health indirectly because some diseases are suggested to be linked to alterations in the bacterial community [49,50,51,52,53,54,55,56,57]. Moreover, phages, including temperate ones, may also modulate eukaryotic cell functions and human immune response by inducing, among others, phagocytosis, cytokine production, and leukocytes activation, as well as the polarization of macrophages [58].
噬菌体有两种主要的生命周期：溶解和裂解。在溶解循环中，细菌细胞被完全破坏。这些噬菌体（溶解性、毒性）利用宿主细胞机制复制和组装新的噬菌体病毒。另一方面，温带噬菌体喜欢溶菌循环，它们的生命周期建立在将自己的遗传物质与宿主基因组整合的能力上，并以所谓噬菌体的形式转入潜伏阶段。这类噬菌体也能在特定条件下进入溶解循环，溶解细胞，并向环境释放后代病毒。据报道，栖息在人类和动物体内的噬菌体更倾向于溶解循环[45, 46]。相比之下，水生生态系统中的噬菌体更喜欢典型的 “杀-赢 “动态[46, 47]。造成这种情况的原因尚不清楚，但 Knowles 等人假设，人体生态系统与水生生态系统之间的极性是基于这样一种观察，即温带噬菌体在多样化的生态系统中变得越来越重要，尤其是在微生物密度较高的生态系统中[48]。这些噬菌体可以通过转座、诱导和水平基因转移（HGT）来调节细菌的基因表达并改变其表型。温带噬菌体还可以在细菌细胞之间转移毒力基因或抗生素耐药性基因。庞大的基因库可以塑造细菌的多样性和功能；因此，噬菌体对细菌的平衡和平衡做出了贡献。病毒体（主要是噬菌体）组成的变化会间接影响人类健康，因为有些疾病被认为与细菌群落的改变有关[49, 50, 51, 52, 53, 54, 55, 56, 57]。此外，噬菌体（包括温带噬菌体）还可能通过诱导吞噬、细胞因子产生、白细胞活化以及巨噬细胞极化等方式调节真核细胞功能和人体免疫反应[58]。
Current research suggests that the composition of the gut phageome is highly individualistic, as it consists mostly of long-term colonizing temperate phages [59], but it has also been shown to change throughout the human lifespan. It adapts to our microbiota and changes by affecting not only bacterial hosts but also the human organism by modulating immune response [59,60,61,62,63]. After birth, phage content and diversity are extremely low. However, this changes during the early stages of life, when the human phageome is highly dynamic. Initially, it is dominated by dsDNA tailed bacteriophages, representing sipho-, podo-, and myovirus morphotypes, previously classified (before major changes to bacteriophage taxonomy, reflecting genomic relationships rather than morphology-based classification) as members of—now abolished—Siphoviridae, Podoviridae, and Myoviridae, respectively. Phages belonging to the Microviridae family (ssDNA) were also detected. During infancy, viral and bacterial composition undergo dynamic modifications. Interestingly, the greatest richness and diversity of gut bacteriophages is observed within the first four days of life, and subsequently decreases over time, reaching stability in adulthood [64]. Additionally, it can be disturbed by different factors, such as diet, lifestyle changes, or diseases [65,66,67]. The gastrointestinal tract as well as other human body surfaces are lined with a mucosal layer, utilized by microbes to inhabit and to communicate with the host [68]. Bacteriophages populate mucosal surfaces by binding to mucin glycoproteins through immunoglobulin-like spikes present on their capsid in a process referred to as bacteriophage adherence to mucin (BAM). This phenomenon is believed to most likely play two significant roles: protection from pathogenic bacteria for the human host and providing lysogens with an environment to develop a bacterial symbiotic relationship that benefits the human host [62,65,66].
目前的研究表明，肠道噬菌体组的组成高度个性化，因为它主要由长期定植的温带噬菌体组成[59]，但研究也表明，它在人的整个生命周期中都会发生变化。它适应我们的微生物群，并通过调节免疫反应不仅影响细菌宿主，也影响人类机体[59, 60, 61, 62, 63]。出生后，噬菌体的含量和多样性极低。然而，这种情况在生命的早期阶段发生了变化，此时人类的噬菌体群高度活跃。最初，噬菌体组主要由dsDNA尾部的噬菌体组成，分别代表虹吸病毒、荚膜病毒和肌病毒形态，它们以前（在噬菌体分类学发生重大变化之前，反映的是基因组关系而不是基于形态的分类）分别被归类为虹吸病毒科、荚膜病毒科和肌病毒科的成员–现在这些分类已被废除。此外，还检测到属于微小病毒科（ssDNA）的噬菌体。在婴儿期，病毒和细菌的组成发生了动态变化。有趣的是，肠道噬菌体的丰富性和多样性在婴儿出生后的头四天达到最高，随后随着时间的推移逐渐减少，到成年时达到稳定[64]。此外，饮食、生活方式改变或疾病等不同因素也会干扰肠道噬菌体的多样性[65, 66, 67]。胃肠道和其他人体表面都有一层粘膜，微生物利用这层粘膜栖息并与宿主交流[68]。噬菌体通过其菌盖上的免疫球蛋白样尖峰与粘蛋白糖蛋白结合，从而在粘膜表面繁殖，这一过程被称为噬菌体粘附粘蛋白（BAM）。这种现象被认为很可能起到两个重要作用：保护人类宿主免受病原菌的侵害；为溶菌体提供发展细菌共生关系的环境，使人类宿主受益[62, 65, 66]。
Reyes et al. (2010) performed a metagenomic analysis of human gut viromes and demonstrated that the fecal virome is highly diverse, while interpersonal viral diversity remains relatively low [46]. Moreover, up to 80% of virome reads generated in that study did not match any known sequences in public databases, which highlights the difficulty in identifying bacteriophage communities and the limitations of these estimates. Interestingly, Dutilh et al. (2014) applied a cross-assembly approach for unknown virome sequence data and identified a ~97 kb circular genome of a novel dsDNA phage named “CrAssphage” [67,68]. It is highly abundant and ubiquitous in all human fecal samples amplified using Bacteroides intestinalis [69]. Manrique et al. (2016) proposed the term “healthy gut phageome”, which consists of core and common phages present in healthy individuals that are likely globally distributed [61]. According to the authors, it is generally dominated by temperate tailed phages (formerly grouped in the—now abolished—order Caudovirales, currently replaced on the higher taxonomic level with the class Caudoviricetes [70,71]) and lytic Microviridae bacteriophages [72,73], while in phage dysbiosis the gut phageome has an increased number of lytic phages and/or activated prophages [74]. The change in phageome composition may stimulate the development of life-threatening diseases or progression into a more severe state of diseases, such as periodontal disease, Parkinson’s disease, type 2 diabetes, cancer, or gastrointestinal disease [74,75,76,77,78,79]. Interestingly, it has been observed that there is a significant decrease in core bacteriophages in patients with gastrointestinal diseases such as Crohn’s disease or ulcerative colitis [61]. At the same time, the occurrence of these diseases was correlated with the expansion of pathogenic Proteobacteria (e.g., Escherichia coli, Fusobacterium) and reduced number of protective bacteria (e.g., Faecalibacterium prausnitzii, Rumininococci) [80,81,82]. An increasing number of research articles suggest that alterations in the gut phageome may be associated with diet, inflammatory bowel disease, malnutrition, or obesity, but it is important to highlight that it is still unknown whether they are simply a consequence of changes in the gut microbiota or they are directly implicated in these pathological states [63,83,84,85].
Reyes等人（2010年）对人类肠道病毒组进行了元基因组分析，结果表明粪便病毒组具有高度多样性，而人与人之间的病毒多样性仍然相对较低[ 46]。此外，该研究中生成的病毒组读数有高达 80% 与公共数据库中的任何已知序列不匹配，这凸显了确定噬菌体群落的难度以及这些估计值的局限性。有趣的是，Dutilh 等人（2014 年）采用交叉组装方法处理未知病毒组序列数据，发现了一种名为 “CrAssphage “的新型dsDNA噬菌体的约 97 kb 环状基因组[ 67, 68]。它在使用肠杆菌扩增的所有人类粪便样本中含量高且无处不在[ 69]。Manrique 等人（2016 年）提出了 “健康肠道噬菌体组”（healthy gut phageome）一词，它由健康个体中存在的核心噬菌体和常见噬菌体组成，这些噬菌体可能分布于全球[ 61]。根据作者的说法，健康肠道噬菌体组一般以温带尾状噬菌体（以前归入现已废除的 Caudovirales 目，目前在更高的分类学层面被 Caudoviricetes 类取代[70, 71]）和溶解性微病毒科噬菌体[72, 73]为主，而在噬菌体菌群失调的情况下，肠道噬菌体组中溶解性噬菌体和/或活化原生噬菌体的数量会增加[74]。噬菌体组组成的变化可能会刺激危及生命的疾病的发生，或使疾病发展到更严重的状态，如牙周病、帕金森病、2 型糖尿病、癌症或胃肠道疾病[74, 75, 76, 77, 78, 79]。有趣的是，据观察，克罗恩病或溃疡性结肠炎等胃肠道疾病患者体内的核心噬菌体明显减少[61]。同时，这些疾病的发生与致病性变形杆菌（如大肠杆菌、镰刀菌）的增加和保护性细菌（如普氏粪杆菌、反刍球菌）数量的减少有关[80, 81, 82]。越来越多的研究文章表明，肠道噬菌体组的改变可能与饮食、炎症性肠病、营养不良或肥胖有关，但必须强调的是，目前还不清楚它们仅仅是肠道微生物群变化的结果，还是直接与这些病理状态有关[63, 83, 84, 85]。