The Viruses of the Gut Microbiota

Abstract

The gut virome is the viral component of the gut microbiome. Knowledge regarding its composition, interindividual and temporal variability is increasing, and the significance of its impact on human health, both in homeostasis and disease is being recognized. Here we review the recent advances in this field, and the questions that arise in the context of the rapidly increasing information regarding its composition and function. With the extending collection of human data, the power of next generation sequencing, and functional studies, the factors that influence the composition of the gut virome and its impact on human health will be further refined in the coming years.

The very rapid increase in untargeted Next Generation Sequencing usage in the field of microbiology has allowed to increase the knowledge of resident and pathogenic viruses, and characterize previously unknown or variant viruses. Technological pipelines uncover viruses referenced in databases with a threshold of sensitivity equivalent to that of quantitative PCRs, and are now becoming even more sensitive than PCR with the increasing depth of sequencing [1], [2], [3], [4]. This type of pipeline also allows acquisition and assembly of de novo full-length genomes from biological samples, and thereby the discovery of new viruses, even when very distant from known viruses (for a recent review see Ref. [5]). These tools have begun to reveal the existence and composition of the human gut virome and unravel its intrinsic complexity, and interindividual variability in healthy individuals. Yet, the precise composition and potential impact on health of the human virome remains to be determined.

The eukaryotic virome, a component of the gut microbiome

The gut virome is defined as the viral component of the gut microbiome, defined itself as the microbial communities of the gut. The gut virome is composed of eukaryotic viruses able to replicate in human cells, as well as bacteriophages that replicate in gut bacteria, which are the most abundant. Eukaryotic viruses also come from food intake, like plant [6] and animal [7] viruses. Systematic longitudinal studies are still lacking and it is therefore difficult to distinguish with certainty viruses that establish long-lasting infection and can be considered as members of a standard flora, from those responsible for acute infections, in particular for human eukaryotic viruses.

Regarding viruses of bacteria (bacteriophages), their presence is indeed modulated by the presence of their host bacteria and they also might regulate the bacterial contents. Recent reviews [8] have covered the human gut phage communities, showing that the population is highly individual and dominated by DNA phages exhibiting a temperate lifestyle. Nevertheless, phage can also lyze bacteria and impact relative bacterial counts [9], [10]. The viral load is roughly similar to that of bacteria [11]. Phage may vector transduction (gene transfer) between strains and even bacterial species, and therefore deliver genes encoding toxins, virulence factors, or alternate metabolisms. We have focused this chapter on human eukaryotic viruses.

The history of human gut eukaryote viruses has until recently been dominated by the discovery of pathogenic viruses (among which Enterovirus, Rotavirus, Norovirus genus) that generally lead to transient and symptomatic infections, but some eukaryotic viruses seem resident of the human gut [12]. Most gut viruses are not cultivable and unbiased metagenomics studies have therefore contributed recently to their better characterization. The eukaryotic virome seems to be acquired progressively with age, in contrast to bacteriophage richness, which seems greatest early in life and then decreases [13]. Acquisition of these resident viruses is associated in healthy infants to no apparent underlying acute or chronic disorders [13]. Enteroviruses, parechoviruses, and sapoviruses were mostly detected. Comparison of the sequences of enterovirus and parechovirus strains from cotwins showed high identity, suggesting that twins harbor similar virome, in part linked to common exposure [13].

Later in age, persistent or intermittent shedding of resident enteric viruses from healthy people is well established. For example, human enterovirus (EV) [14] and parechovirus (HPeV) [15] are excreted by a large fraction of healthy children under the age of five. A 1-year NGS longitudinal study of the stool of two healthy infant siblings in samples taken at 1-week intervals demonstrated that viruses were continuously excreted [16]. The most frequently observed viruses, in decreasing order, were anellovirus (TTV but also TTMV), picobirnavirus, and HPeV types 1 and 6. Bocavirus (HBoV-1), Adenovirus C and F, Aichi virus, astroviruses, and rotaviruses were less frequently detected. Surprisingly, other enteric viruses, such as noroviruses, coronaviruses, cardioviruses, cosaviruses, saliviruses, and sapoviruses, were not detected, although they are frequently detected in stool, indicating that the results of this survey only provide a first indication of the composition of the gut virome, which would benefit from the study of larger samples. Some viruses, including adenoviruses, anelloviruses, picobirnaviruses, parechoviruses, and Human bocavirus, were shed for months. These viruses are more likely to represent a significant portion of the normal human virome, owing to their ability to establish persistent infections. Among these viruses, another study showed that the presence of anelloviruses and circoviruses discriminate twin pairs that include one child with severe acute malnutrition from concordant healthy pairs, but not diseased versus healthy children within a given twin pair. So, it remains unclear if anelloviruses and circoviruses are markers of, or are responsible for, disease pathogenesis [17].

Interplay between gut virome and immune system

The interplay between the virome and the immune system is far from being fully understood. Phage and eukaryotic viral particles are translocated, and independently of replication can activate innate immunity. Physical abundance of phages over eukaryotic human viruses, nevertheless, suggests that such activation is mainly driven by phages. Detection of corresponding viral nucleic acids within cells through several pattern-recognition sensors for RNA (RIG-I and Toll-like receptors TLR7 and TLR8) and DNA (TLR9, cyclic-GMP-AMP) should lead to expression of type interferon (IFN)-α and -β with pleiotropic activities, and inflammatory cytokines, such as interleukin 1 and 6. It has been suggested that such activation of innate immunity could have a positive effect against pathogenic infections [18], as already demonstrated for systemic persistent cytomegalovirus infection [19].

On the other side, it has been shown recently that, quite surprisingly, viruses could also play a beneficial role in the control of gut inflammation. Resident viruses recognized by TLR3 and TLR7 favor intestinal homeostasis through antiinflammatory cytokines as IFN-β secreted mainly by plasmacytoid dendritic cells [20].

Immune impairment has been shown to modify the enteric virome [21], [22]. The enteric eukaryotic virome expands during pathogenic SIV infection of rhesus macaques [21]. In HIV-infected patients, there is a relationship between low peripheral CD4 T cell counts and alteration of the virome [23]. Interestingly, an association was evidenced between enteric adenovirus and both advanced HIV/AIDS [23], and SIV-infected macaques [21], [22]. This suggests a mechanism where adenovirus replication promotes mucosal lesions and enteropathy leading to bacterial and bacteriophage translocation that promotes chronic immune stimulation.

The extent by which immunosuppressed patients harbor pathogenic and opportunistic viruses in the gut is currently unknown. It is likely, however, that a large number of viral species coexist and persist, and may be transiently cleared to reappear later, in the absence of protective immunity. Prospective longitudinal studies aimed at characterizing at steady state in healthy and immunosuppressed individuals the dynamics of the gut virome are warranted, not only to better characterize the driving forces that shape the gut microbiome, but also to monitor and ideally predict pathogenesis associated with these viruses, and ideally prevent their transmission to other susceptible hosts.

Pathogenic viruses of the gut virome: enteropathogenic viruses associated with systemic infections

Foodborne viral infections are associated with the presence of infectious viral particles in the gut, and enteropathogenic viruses are therefore either transiently, and in a prolonged manner, present in the gut and part of the gut virome. As for foodborne bacterial infections, which may lead to local intestinal infection, or systemic disease, viruses whose portal of entry is the gut may be associated with either local or systemic disease. Their transmissibility depends on the amount of infectious viral particles released in the feces, and the duration of the viral release. Rotavirus and noroviruses, which replicate in intestinal epithelial cells, lead to local replication in the digestive tract, and very high-level fecal shedding, which is favored by the associated diarrhea, which mechanism can result, as for bacteria, from the action of a toxin [24] or a direct enteropathogenicity, and accounts for their high transmissibility. In contrast, enteroviruses, the leading cause of meningitis, translocate at the gut level and disseminate systemically. While their cell tropism is broader, their replication in mucosal tissue and their release in the intestinal lumen lead to fecal shedding, release in the environment and transmission. The infective potential of enteric viruses depends on the species itself, microbiota, and many host factors, such as age, nutritional status, and immune functions, which are themselves dependent on the microbiota. This underlines the complex interplay between the host, and the bacterial and viral parts of the microbiome, which only begins to be deciphered.

Gut as a major source of neurotropic viruses, when pathogenesis and shedding is favored by humoral immune deficiency

The composition of the gut virome may vary according to multiple factors, such as exposure to viral species, the composition of the microbiota, and host factors, such as immune functions. It is well known by clinicians in charge of immunodeficient patients that diarrhea is a frequent symptom associated with opportunistic viral infections. Patients under immunosuppressive therapy for organ transplantation may present with chronic diarrhea associated with noroviruses and sapoviruses, leading to chronic fecal shedding, and nosocomial transmission [25]. Patients with congenital agammaglobulinema or profound hypogammaglobulinemia are prone to chronic and recurrent severe enterovirus infection, associated with encephalitis. These patients are frequently persistently colonized with enteroviruses, which can persist for years in the gut, and be associated with multiple episodes of CNS disease. In these patients, the occurrence of encephalitis in the absence of detectable enterovirus by RT-PCR methods in the CSF does not rule out their presence. NGS is indeed able to detect enterovirus genome when RT-PCR is negative, because of its intrinsic sensitivity, and its ability to detect variants that may not be amplifiable by PCR (our unpublished results). Interestingly, astroviruses, which are known to induce enteritis in human have also recently been associated with encephalitis in the context of profound humoral deficiency, underlining the intestine as a reservoir for neurotropic viruses [25a], [25b], [25c]. Another example of virus associated with gastrointestinal infections leading to meningitis and encephalitis are parechoviruses, and in particular human Parechovirus 3 [26].

Yet the large number of enteric viruses species, their broad host tropism, the quasispecies nature of Picornaviridae within a given host, their capacity to recombine, their high transmissibility, and their interactions with the host microbiota and immune functions illustrate not only the fascinating evolutionary success of enteroviruses, but also the complexity of understanding all the factors to take into account to make sense of the contribution of a single viral species to the gut virome.

An uncertain status for diet-derived animal viruses

The human gut virome is also composed of animal viruses transmitted by the oral route by consumption of contaminated food. Hepatitis E virus (HEV) is typically responsible for acute hepatitis in humans. Genotypes 1 and 2 are human specific but type 3 and type 4 have a reservoir in pigs [27]. The virus can be seen as a typical zoonotic virus in the context of acute infections. Nevertheless, long-term chronic infections have been described in immunocompromised patients, highlighting the importance of the host-immune status on virome composition and its potentially pathogenic properties [28], [29]. Animal genotypes 3 and 4 frequently infect humans from the animal reservoir (up to 50% of the population is antibody positive in some areas [30]), and might be adapting to humans. The situation is puzzling for gyroviruses. The first gyrovirus in humans (HGyV), which is part of the Circoviridae family, was initially found by NGS at the surface of the skin of healthy people [31]. It was later shown that different gyroviruses, including a very similar virus, AGV2, are very prevalent in chickens and in human stools [32], [33]. This owns to cross-species transmission of gyroviruses and their replication in humans, or alternatively to passive transit of animal viruses via food intake, as has been observed for plant viruses [6]. Within the Circoviridae family, the cycloviruses constitute a new genus and are found in the feces of humans and other animal species, pose similar questions as gyroviruses. [34]. It is noteworthy that gyroviruses harbor an apoptin gene, which encodes a protein that has the rare property of being specifically cytotoxic for cancer cells. Indeed, natural infection could be of benefit in controlling the development of tumor cells [35], in particular colon cancer (Table 21.1 ).

Table 21.1.

Eukaryotic Viruses of the Human Gut

Family	Genus	References
Picornaviridae	Enterovirus	[36]
	Parechovirus	[36]
	Cardiovirus	[37]
	Salivirus	[38]
Picobirnaviridae	Picobirnavirus	[16]
Astroviridae	Astrovirus	[39]
Reoviridae	Rotavirus
Caliciviridae	Norovirus	[40]
	Sapovirus	[41]
Adenoviridae	Mastadenovirus C and F, and others	[42]
Anelloviridae	Anellovirus	[16]
Cycloviridae	Circovirus	[43]
	Cyclovirus	[43]
Parvoviridae	Bocavirus	[44], [45]

Recent reviews or informative papers are cited when available.