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Introduction
In this post we will be summarising multiple different articles looking at the biology of bacteriophages and their potential applications, with a focus on exploring what we can do to harness their potential. We will start by introducing the most common bacteriophages of the microbiome, and moving onto how these interact and manifest within the microbial communities of the skin, and then concluding with a discussion about whether we can harness them to develop technologies that can engineer the skin microbiome as a way to treat dermatological conditions that affect millions of people annually. We will primarily focus on the sebaceous (oily) sites of the skin such as the face, even though there are indeed a variety of other sites which are also important to consider when looking at phageomes and disease.
The Virome
To understand the role of bacteriophages, it is necessary to first look at defining the virome in relation to host health and microbiome ecology. The virome can be defined as ‘a subset of the core human microbiome consisting only of the viral biomass in a given community’. This applies to the skin also, which is colonised by numerous groups of viruses with their own ecology and interactions. It includes many different classes of virus, the three most common being Eukaryotic DNA viruses, Viral Genetic Elements and Bacteriophages (Phages) (Virgin, 2014).
Virome composition is shaped by a variety of forces, both ecological and evolutionary. Some studies have found that the skin microenvironment, including physical properties (e.g. whether the skin is dry, moist or sebaceous) which appear to be a key driving force behind viral community dynamics (Byrd et al., 2018), with viral blooms appearing in specific sites along the skin including sebaceous regions of the face such the cheeks and the forehead (Oh et al., 2016). Other factors which might impact a person’s microbial community include geography such as pollution levels and UV exposure, in addition to lifestyle factors such as diet, health and personal care.
However, it is important to note here that no core DNA virome has yet been found to exist, with lots of individual variation in virome composition. This could be due to a number of different factors, including biogeography of the skin, ethnicity, genetics, parental imprinting and transmission between and across populations (Byrd et al., 2018). Individual variation of the types of virus found in humans presents a possible future avenue of study to further explore why and how this is the case, and furthermore whether it has any key implications for individual differences in skin conditions.
The Phageome
Despite this lack of a cohesive virome in the human population, there does appear to be a subset of this community which possesses a more concerted signature than its larger counterpart. This is where the phageome comes in. The phageome refers to the net biomass of bacteriophages found within the human microbiome (Townsend et al., 2021). It differs from the virome in that it has been found to possess a conserved signature across human populations, despite any interspecific differences which may exist within the microbiome as a whole, therefore indicating the possibility of a shared core phageome existing (Oh et al., 2016). Bacteriophages fall under the umbrella of the phageome, and are described as ‘viruses which are capable of infecting and/or killing bacteria’ (Castillo et al., 2018). In the case of most humans, the bacteria on the skin microbiome are primarily infected by two core groups of phages found across sebaceous sites of the skin; Cutibacterium phages and Staphylococcus phages. These phages can be found across sebaceous areas of the face, usually with a single strain of phages dominating these sites. Like other phages, their populations tend to remain largely stable within their microenvironments compared to the transient eukaryotic DNA viruses, which suggests a level of fixation within their bacterial-host population (Oh et al., 2016).
In regards to the types of interactions which manifest between bacteriophages and their respective host, these can vary depending on the evolutionary adaptations to the host species they decide to colonise (Hannigan et al., 2015). Interactions usually range from lysogenic, to pseudolysogenic, or purely lytic. Lysogenic phages integrate into the host genome as a prophage and continue to propagate in this form as the host replicates and divides, meaning that their fitness is ultimately linked to the survival of their bacterial host. On the other hand, pseudolysogenic phages can alternate between the two extremes, existing as prophages until they are exposed to environmental stress at which point they are excised and circularised to enter the lytic stage. Finally, the lytic viruses are a group which infect and kill the host while using them as a medium of replication, these types may go onto wipe out large populations of bacteria within a community causing dysbiosis that affect the human host, or in some cases having the opposite effect of preventing pathogenic bacterial species from propagating in the microbiome.
C. acnes and The Skin
C. acnes phages is a subset of Cutibacteria-infecting phages which colonise sebaceous areas of the body, such as the face, with most individuals possessing a single strain of this phage within the skin microbiome (Castillo et al., 2018). C. acnes phages, like many other Cutibacteria-infecting species, tend to be lacking in genetic diversity, with between 85 - 100% sequence identity observed between strains (Liu et al., 2015). Its presence is usually found associated with that of its target bacterial species, C. acnes, with which they form antagonistic interactions, going on to have a reductive effect on bacterial abundance and population size (Oh et al., 2016). Such antagonistic dynamics have played a role in modulating the position of the microbiome through the selective removal of certain C. acnes populations. However, the population sizes of some C. acnes have been found to positively correlate with phage prevalence, this indicates a certain amount of variability of the type of interaction which manifests between the two partners (Oh et al., 2016).
These phages tend to assume a mostly lytic state, going onto infect and lyse their target host cells and effectively reduce the population size of C. acnes species within the microbial community. However, some have been observed to have the ability to adopt a pseudolysogenic state. This shows that the type of bacteriophage that manifests is largely constrained by C. acnes lineage (Liu et al., 2015). This level of flexibility in C. acnes phage lifestyle could have evolved in order to enhance phage survival, but no comprehensive explanation has yet been uncovered for this.
The overpopulation of certain C. acnes strains is associated with skin conditions such as acne. C. acnes phages are capable of lysing and destroying C. acnes strains from most lineages including pathogenic strains which can have the effect of reducing the relative abundance of C. acnes in the host microbiome by shifting the skin microbiome away from acne-associated dysbiosis (Liu et al., 2015).
Additionally, C. acnes phages are more abundant in the facial skin samples of the individuals with healthy, non-acne infected skin, indicating the regulatory function of these phages in preventing proliferation of pathogenic C. acnes strains associated with the onset of acne (Liu et al., 2015). These findings suggest a link between phage abundance and the development of acne, and the role of these bacteriophages in regulating microbiome balance.
S. aureus Phages and The Skin
Staphylococcus aureus phages form interaction with Staphylococcus aureus strains of bacteria that are also highly abundant within the microbiome of sebaceous skin sites. These bacteria have been associated with the onset of many skin diseases, such as atopic dermatitis and psoriasis (Natarelli et al., 2023). Infection of these S. aureus strains by phages has also recently been linked as another potential risk factor in increasing the virulence of these bacterial strains, with phages helping to facilitate transmission of antibiotic resistant genes and virulence factors to these bacteria from other host reservoirs that harbour these genetic elements such as S. epidermidis (Hannigan et al., 2017). This allows these bacteria to fortify their defences against the human immune system, and cause disorders associated with the skin or in some cases even increase severity of skin-disorders.
Many of these lysogenic S. aureus phages carry virulence factors that upon integration into the host genome can confer fitness benefits such as host propagation and survival. They can also carry many genes that might add to this fitness or cause genomic rearrangements that enhance the pathogenicity and virulence of S. aureus strains, going onto improve host fitness and survival and worsening the severity of certain skin conditions as these bacteria grow (Hannigan et al., 2017). The effects of this lysogeny on human skin has to some extent been associated with atopic dermatitis, with greater abundances of S. aureus being detected in patients possessing these lesions (Bjerre et al., 2021).
Potential Applications of Phages
We will now go on to explore the potential applications of these phages, and discuss technologies that have been devised to harness the power of some bacteriophages in the treatment of skin conditions such as acne or atopic dermatitis. It is important to note that suitable candidates for phage therapy must be lytic, non-lysogenic, and free of virulence factors and antibiotic resistant genes in order to properly target these problem strains without transferring virulence factors or genetic elements that might cause the bacteria being targeted more infectious (Kim et al., 2022).
Acne and C. acnes phage therapy
In the case of acne it is increased sebum production that can induce the growth of pathogenic C. acnes strains and this overgrowth is what might exacerbate the conditions and drive inflammation across the skin and bring about global effects (Natarelli et al., 2023). The overpopulation of these strains can go on to trigger dysbiosis by further reducing the already low levels of microbiome diversity, including wiping out other C. acnes populations regardless of whether they are commensal or pathogenic. This phenomenon suggests that acne might have less to do with increasing pathogenic C. acnes strain abundance, but rather it is the loss of C. acnes phylotype diversity in the microbiome (Mias et al., 2023). Certain C. acnes strains have been found to be more strongly associated with acne pathogenesis, while others are associated with healthy skin microbiome composition, this indicates that certain C. acnes phages can be used to target C. acnes bacterial population types associated with acne allowing the selective suppression of bacterial growth while still maintaining commensal or beneficial strain population structure (Fitz-Gibbon et al., 2013; Liu et al., 2015). Personalised phage therapies might also be developed to target particular strains of C. acnes present in the skin microbiome depending on individual bacterial community structure, in order to restore dysbiotic skin. Resistant C. acnes strains might require some more engineering of phages to be able to overcome host immune mechanisms and anti-virulence factors. However, preliminary studies attempting to treat pathogenic C. acnes strains with specific bacteriophages have already shown some promising results (Xuan et al., 2023), with near total population reduction upon application of these phages (Kim et al., 2019). Therefore, showing the potential to treat, or at least minimise, the effects of acne.
Atopic dermatitis and S. aureus phage therapy
In the case of atopic dermatitis, disease can also be brought about by dysbiosis of the skin microbiome. An overabundance of S. aureus populations relative to other species can trigger atopic dermatitis, by causing immune dysregulation and impairing the skin barrier function which leads to inflammation and flaking of the skin which is characteristic of this condition (Tham et al., 2020). The symptoms of AD can be worsened through the acquisition of virulence genes from bacteria that increase S. aureus strains pathogenicity. While some strains of phage support and promote the survival of S. aureus, a variety of other groups have been proven to have powerful anti S. aureus agents with several cases reporting complete eradication of S. aureus and/or patient improvement upon administration of these phage strains (Hatoum-Aslan, 2021). Many of these phages have small genomes which are too compact to support the integration of virulence-associated genes that can be transferred between the microbiome during transduction, thus eliminating the risk of increasing pathogenicity or inducing mutations. These can be engineered to express antibacterial compounds in their genomes that have the effect of destroying the infected cell upon expression (Hatoum-Aslan, 2021). Other studies have also demonstrated the effect of phage derived compounds against AD, showing the potential of specific S. aureus phages in combating these AD associated bacterial strains (Tham et al., 2020).
The Potential of Phage Therapy
Acne and atopic dermatitis industries in the US alone are worth $2.5 billion (Castillo et al., 2018) and $5 billion (Adamson, 2017) respectively, with treatments often being costly and difficult to develop. These conditions present a fresh, untapped market in which phage therapies can enter. Phage therapies can offer an alternative to traditional methods of treatment of bacterial infections requiring the use of antibiotics. This is especially important when considering the global burden of antibiotic resistance and the rising numbers of resistance annually observed, and demonstrates how antibiotics are not a sustainable method of treating many bacterial infections. These phages can be made to target bacteria that have developed some level of multidrug resistance, which presents the potential of them also reducing antibiotic resistance in a population and making the administration of antibiotics all the more effective (McCutcheon et al., 2020). Unlike traditional medicines, bacteriophage therapy is able to treat diseases in a target specific manner, without harming other components of the microbiome or human host. They are also easier and less expensive to produce en masse (Jończyk-Matysiak et al., 2017), therefore they are practical, economically feasible and able to cover a large area of the skincare market. Most importantly, as a natural part of the human microflora, they are safe and well tolerated with no adverse effects of their administration being reported as of yet (Castillo et al., 2018).
Future Perspectives
Phage therapy, as with all budding technologies, still has a considerably long way to go before it can become a conventional treatment for dermatological conditions. More research on the interactions between bacteriophages and the skin microbiome must be conducted to investigate any global effects which might be observed upon removal of any particular bacteria subpopulation, particularly as this is something which might have adverse effects that we are currently unaware of (Castillo et al., 2018). It will also help us get a better understanding of the extent to which these phages produce such bactericidal in regulatory effects on the microbiome. This will also help to identify the right phages in targeted treatment.
Despite impressive findings surrounding the effectiveness of phages in removing disease-associated micropopulations, none of these involve the use of human models as a basis of study. Indeed, the conduction of more human trials are necessary before this field can expand and move forward towards being released to the market (Jończyk-Matysiak et al., 2017; Castillo et al., 2018).
Caution must also be exercised when taking phage species which express a certain level of lysogeny within their strains, such as those strains targeting S. aureus. These lysogenic phages can have the opposite effect of reinforcing pathogenic bacteria, rather than having the desired effect of destroying them (Jończyk-Matysiak et al., 2017).
The long term impact of population wide eradication on the microbiome health and ecology is not yet fully understood or characterised. This ultimately means we must proceed with caution moving forward. However, many remain optimistic that this technology will move forward to have transformative effects on the skin and healthcare industry, presenting an exciting new avenue for disease to be targeted and treated more efficiently than ever before. Improvements in technology and recent advances in our understanding of phage biology have certainly made it more likely for these expectations to one day become a reality.
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