A phageome is a community of

bacteriophage A bacteriophage (), also known informally as a phage (), is a virus that infects and replicates within bacteria. The term is derived . Bacteriophages are composed of proteins that Capsid, encapsulate a DNA or RNA genome, and may have structu ...

s and their metagenomes localized in a particular environment, similar to a

microbiome A microbiome () is the community of microorganisms that can usually be found living together in any given habitat. It was defined more precisely in 1988 by Whipps ''et al.'' as "a characteristic microbial community occupying a reasonably wel ...

. Phageome is a subcategory of

virome Virome refers to the assemblage of viruses that is often investigated and described by metagenomic sequencing of viral nucleic acids that are found associated with a particular ecosystem, organism or holobiont. The word is frequently used to d ...

, which is all of the viruses that are associated with a host or environment. The term was first used in an article by Modi ''et al.'' in 2013 and has continued to be used in scientific articles that relate to bacteriophages and their metagenomes. A

, or phage for short, is a virus that can infect bacteria and archaea, and can replicate inside of them. Phages make up the majority of most viromes and are currently understood as being the most abundant organism. Oftentimes scientists will look only at a phageome instead of a virome while conducting research. Variations due to many factors have also been explored such as diet, age, and geography. The phageome has been studied in humans in connection with a wide range of disorders of the human body, including IBD, IBS, and colorectal cancer.

In humans

Although bacteriophages cannot infect human cells, they are found in abundance in the

human virome The human virome is the total collection of viruses in and on the human body. Viruses in the human body may infect both human cells and other microbes such as bacteria (as with bacteriophages). Some viruses cause disease, while others may be asy ...

. Phageome research in humans has largely focused on the gut, however it is also being investigated in other areas like the skin, blood, and mouth. The composition of phages that make up a healthy human gut phageome is currently debated, since different methods of research can lead to different results. At birth, the human phageome, and the overall virome in general, is almost non-existent. The human phageome is thought to be brought about in newborns through prophage induction of bacteria passed on from the mother vaginally during birth. However, phages can be introduced through breastfeeding, made evident through studies finding near-exact matches of ''crAssphage'' sequences between mother and child. Variations in the human gut phageome continue across the lifespan. ''

Siphoviridae ''Siphoviridae'' was a family of double-stranded DNA viruses in the order '' Caudovirales''. The family ''Siphoviridae'' and order '' Caudovirales'' have now been abolished, with the term siphovirus now used to refer to the morphology of viruses ...

'' and ''

Myoviridae ''Myoviridae'' was a family of bacteriophages in the order '' Caudovirales''. The family ''Myoviridae'' and order '' Caudovirales'' have now been abolished, with the term myovirus now used to refer to the morphology of viruses in this former famil ...

'' are the most abundant in infants and their numbers wane into childhood, whereas '' Crassvirales'' dominate in adults. The phageome can also experience changes as a result of diet, which can introduce new phages present in our foods. For example, in those with gluten-free diets, ''crAssphage'' were noted in higher abundance along with decreases in the families of ''

Podoviridae Podoviridae was a family of bacteriophage in the order '' Caudovirales'' often associated with T-7 like phages. The family and order '' Caudovirales'' have now been abolished, with the term podovirus now used to refer to the morphology of viruses ...

''. Global geographical differences in phageome composition have been noted, with further variation found within individuals living in rural and urban locations. For instance, residents in Hong Kong, China were found to have less phages associated with targeting pathogenic bacteria in comparison to those in Yunnan province. Furthermore, residing for longer periods of time in urban regions correlated with increases of ''Lactobacillus'' and ''Lactococcus'' phages.

In disease

Changes in the phageome have been seen in various disorders affecting the human body. In the gut, unique changes in the phageome have been described in both

inflammatory bowel disease Inflammatory bowel disease (IBD) is a group of inflammatory conditions of the colon and small intestine, with Crohn's disease and ulcerative colitis (UC) being the principal types. Crohn's disease affects the small intestine and large intestine ...

and

irritable bowel syndrome Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder characterized by a group of symptoms that commonly include abdominal pain, abdominal bloating, and changes in the consistency of bowel movements. These symptoms may ...

. Even further specific changes exist in subtypes of the two disorders. IBS subtypes of IBS-D and IBS-C saw increases in different species belonging to '' Microviridae'' and ''Myoviridae''. In

Ulcerative colitis Ulcerative colitis (UC) is one of the two types of inflammatory bowel disease (IBD), with the other type being Crohn's disease. It is a long-term condition that results in inflammation and ulcers of the colon and rectum. The primary sympto ...

and

Crohn's disease Crohn's disease is a type of inflammatory bowel disease (IBD) that may affect any segment of the gastrointestinal tract. Symptoms often include abdominal pain, diarrhea, fever, abdominal distension, and weight loss. Complications outside of the ...

, which are subtypes of IBD, differences in levels of ''

Caudovirales ''Caudoviricetes'' is a class of viruses known as tailed viruses and head-tail viruses (''cauda'' is Latin for "tail"). It is the sole representative of its own phylum, ''Uroviricota'' (from ''ouros'' (ουρος), a Greek word for "tailed" + ...

'' richness and species have been found. Furthermore, phages that target ''

Acinetobacter ''Acinetobacter'' is a genus of Gram-negative bacteria belonging to the wider class of Gammaproteobacteria. ''Acinetobacter'' species are oxidase-negative, exhibit twitching motility, and occur in pairs under magnification. They are important ...

'' have been found in the blood of patients with Crohn's disease. This is thought to occur due to the compromised, inflamed gut barrier allowing for bacteriophage transfer. In the mouth,

periodontitis Periodontal disease, also known as gum disease, is a set of inflammatory conditions affecting the tissues surrounding the teeth. In its early stage, called gingivitis, the gums become swollen and red and may bleed. It is considered the main c ...

has been associated with ''Myoviridae'' residing under the gums along with a currently unspecified bacteriophage in the ''Siphoviridae'' family. Phageome changes have also been described in metabolic disorders including type-1 diabetes, type-2 diabetes and

metabolic syndrome Metabolic syndrome is a clustering of at least three of the following five medical conditions: abdominal obesity, high blood pressure, high blood sugar, high serum triglycerides, and low serum high-density lipoprotein (HDL). Metabolic syndro ...

. In type-1 diabetes, overall shifts have been seen in ''Myoviridae'' and ''Podoviridae.''{{Cite journal , last=Nabi-Afjadi , first=Mohsen , last2=Teymouri , first2=Samane , last3=Monfared , first3=Fatemeh Nafe , last4=Varnosfaderani , first4=Seyed Mostafa Noorbakhsh , last5=Halimi , first5=Hossein , date=11 August 2023 , title=The Human Gut Phageome: Identification and Roles in the Diseases , url=https://www.scientificarchives.com/article/the-human-gut-phageome-identification-and-roles-in-the-diseases , journal=Journal of Cellular Signaling , language=en , volume=4 , issue=3 , pages=128–141 , doi=10.33696/Signaling.4.100 , issn=2692-0638, doi-access=free The genome of bacteriophages residing in the gut in Type-2 diabetes patients have been shown to contain numerous genes implicated in disease development. Total phage representation in the virome is higher in individuals with Cardiovascular disease than healthy controls, totaling 63% and 18% respectively. Lastly, researchers studying

Colorectal cancer Colorectal cancer (CRC), also known as bowel cancer, colon cancer, or rectal cancer, is the development of cancer from the Colon (anatomy), colon or rectum (parts of the large intestine). Signs and symptoms may include Lower gastrointestinal ...

have observed increased richness in a variety of phage genera, with the most notable differences seen in ''Inovirus'' and ''Tunalikevirus.''

References

Microbiology Bacteriophages Wikipedia Student Program Microbiomes

In humans

In disease

See also

References