## 3 Intestinal Bacteriophages and Faecal Virome Transplants
### The Phageome of the Gut and the Surprising Prevalence of crAssviridae
In the realm of phages specificity, the study has also managed to identify three separate hosts for _Carjivirus communis_, namely _Plocoaeicola vulgaris, Phocaicola dorei_, and _Bacteroides stercoris_, which proves that at least some crAssviruses are characterised by relatively low host specificity and therefore could potentially engage in regulating gut microbiota above species level. During the aforementioned study, no apparent effect of phage addition on bacterial numerosity was noticed, which was consistent with observations about _Jalgtovirus secundus_ by [PERSON] and colleagues. Considering that these viral species are closely related and that both belong to the _Alphacrassvirinae_ subfamily [88], it seems reasonable to consider _Jalgtovirus secundus_ to potentially be a phage-plasmid as well. While further studies are definitely necessary to confirm this hypothesis, it would explain many of the unusual traits of the virus mentioned before, including not forming plaques and not decreasing bacterial counts in liquid cultures in a noticeable way despite high viral titres. This sheds new light on the influence of phages in the gut, as it is possible that many of these are in fact phage-plasmids, therefore possessing high capacity for carrying genetic elements which can significantly influence their hosts--and, by extension, affect the entire microbiome. Many phage-plasmids are capable of conferring antibiotic resistance [92], and some can possess genes aiding infection, functional CRISPR systems to protect the bacterium from further infections, genes encoding crucial enzymes for the biosynthesis of certain metabolites, plasmid maintenance genes and many others [93]_Carjivirus communis_ itself carries infection-supporting genes, a repL gene implicated in plasmid replication, as well as genes predicted to encode a toxin-antitoxin (TA) system that eliminates bacterial progeny which do not inherit the viral plasmid [89]. Moreover, it also contains a fragment which is highly similar to the MobC relaxosome protein gene, crucial for the formation of sex pili in bacteria [89]. It can be therefore assumed that the phage propagates intensely through conjugation, especially when the bacterial population is not under high environmental stress. Further studies are definitely necessary to confirm the presence of similar genes in other crAssviruses, their effective expression in infected cells, and the general prevalence of phage-plasmid lifestyle among gut viruses, especially in animals. Applying this new knowledge to review, reconsider, and possibly update the previously discussed concept of immunity mediated by mucosa-dwelling phages would also be desirable. Nonetheless, utilising the concept of the phage-plasmid lifestyle to explain the previously mentioned peculiarities of crAssviruses seems to be a reasonable approach that reflects their characterisation as persistent and able to significantly influence the gut microflora, therefore justifying the consideration of using virome transplants to stabilise intestinal microbial communities. The presence of viruses exhibiting a phage-plasmid lifestyle in the human gut--capable of both vertical and horizontal gene transmission--suggests their potential role in maintaining microbial network resilience and adaptability. In the context of FVT, their transfer could contribute to restoring functional microbial dynamics, particularly in microbiomes disrupted by antibiotics or infection, even if their direct therapeutic role remains to be fully elucidated. It is also worth reiterating that plaque assays, though widely used, fail to detect many abundant gut phages, including crAsslike and temperate viruses, which often do not form plaques. This limitation highlights the need for metagenomic and alternative culture-independent approaches better suited to capturing the core human gut virome.