## 3 Intestinal Bacteriophages and Faecal Virome Transplants  
### The Phageome of the Gut and the Surprising Prevalence of crAssviridae  
The number of studies describing the gut virome--or, more specifically, the phageome, as most viruses in the human gut are bacteriophages [73]--is not very high. However, current publications shed some light on this issue, revealing some incredibly interesting facts that might be crucial for our understanding of the virus-prokaryote-host dynamics. A superficial glance at the numerosity and diversity of gut phages might lead the observer to question their supposed stabilizing effect on the gut microflora--after all, according to the standard Lotka-Volterra model of predation, one might expect to observe peaks of bacterial numerosity followed by sharp drops as viral counts begin to increase and subsequently peak. While this Lotka-Volterra dynamic is in fact present in the gut of infants [74], the phageome (and indeed, in many cases, the entire microbiome) of the gut tends to remain stable during adulthood [75; 76]. Therefore, a different model for characterising interactions between prokaryotes and viruses in the gut has been developed, which postulates that  
Figure 1: The diagram presents a simplified summary of pipelines for FMT and its derivatives, as well as for FVT, which is described in the following section. gut phages in the outer layers of gut mucosa in healthy, adult hosts are mostly temperate viruses, which tend to integrate with the bacterial genome through the lysogenic cycle and only rarely cause cell death and virion release through cell lysis [77]. These temperate phages can protect commensal bacteria from becoming infected by other phages through a mechanism known as superinfection exclusion [78]. According to the model proposed by [PERSON] and [PERSON], the nutrient-rich environment of the outer mucosa may contribute to rather low lytic activity of the temperate phages. At the same time, virions that do get released after the occasional reactivation of a temperate phage and subsequent lysis of the cell may be deposited in significant numbers in the middle mucus layer, where they are more likely to cause a lytic infection of bacteria that are able to penetrate the mucosa, therefore forming a barrier against pathogens. This characterisation of the role of temperate phages is supported by the fact that they tend to be highly conserved within the microbiome of an individual. According to one study, over 80% of viral contigs found in the gut of a particular adult individual could be identified again after 850 days, and the contigs belonging to temperate phages were characterised by significantly lower nucleotide substitution rates than lytic phages [75]. This might have been caused by the relatively high precision of bacterial polymerases that replicate viral sequences integrated with bacterial genomes and the lower overall replication frequency. Gut viromes of different hosts, similarly to gut bacteriomes, tend to be highly diversified. However (and perhaps surprisingly, given the difficulty in characterising common patterns shared between bacteriomes), there are reports of certain phages that are identifiable in most, if not all, samples taken from different hosts, forming the core phageome of a population. One study identified 23 core bacteriophages that could be found in more than 50% of healthy individuals from several cohorts [79]; a significant decrease in core bacteriophage presence was observed among individuals with ulcerative colitis or [PERSON]'s disease. Even though the results are certainly promising, it is important to note that the data utilised in the study came from typically Western cohorts, geographically located in Boston, Chicago, and Cambridge. One of the most prevalent phage genomes identified in the study, along with three similar genomes, was a virus discovered two years earlier [80] dubbed \"crAssphage\", which owes its name to the \"crAss\" v. 1.2 cross-assembly software used to facilitate its identification in metagenomic data.