Phageome

A phageome is a community of bacteriophages and their metagenomes localized in a particular environment, similar to a microbiome. The term represents a subcategory of virome (the complete collection of viruses associated with a host or environment) that specifically focuses on bacteriophages - viruses that infect bacteria. The term "phageome" was first introduced in scientific literature by Modi et al.

Definition and Composition

The phageome encompasses all bacteriophages present in a specific ecological niche, along with their genetic material. These bacteriophages are extremely diverse in size, morphology, and genomic organization, representing the most abundant biological entities on Earth. The phageome can be studied at various levels, from local environments to host-associated communities.

Host-Associated Phageomes

Human Phageome

The human body harbors countless phage particles due to the extensive human microbiome. The human phageome can be further categorized into:

• Healthy gut phageome (HGP)
• Diseased human phageome (DHP)

The gut phageome in particular has received significant research attention, as bacteriophages are present in the human gut in at least the same numbers as bacteria.

Research Methods

Studying the phageome presents unique challenges due to the diversity and complexity of bacteriophage communities. Primary research approaches include:

1. Metagenomics: The analysis of genetic material recovered directly from environmental samples, allowing researchers to identify and characterize phages without the need for cultivation.

2. Culture-assisted metagenomics: A hybrid approach that combines traditional culturing methods with metagenomic sequencing to discover novel bacteriophages.

3. Bioinformatic tools: Specialized computational methods to identify phage sequences in metagenomic datasets and analyze their diversity.

Ecological and Biological Significance

Phageomes play critical roles in microbial ecosystems:

1. Driving bacterial evolution: Bacteriophages create gene flow networks that fuel ecological adaptations in bacterial communities.

2. Regulating microbial populations: By infecting and lysing specific bacterial hosts, phages contribute to population control and community structure.

3. Horizontal gene transfer: Phages can transfer genetic material between bacteria, contributing to bacterial diversity and adaptation.

Applications and Importance

The study of phageomes has several important applications:

1. Human health: Understanding the relationship between the gut phageome and various diseases, as alterations in the phageome have been associated with gastrointestinal and liver diseases.

2. Phage therapy: The therapeutic use of bacteriophages to treat bacterial infections, particularly those resistant to antibiotics.

3. Biotechnology: Discovery of novel enzymes and genetic elements with potential industrial applications.

4. Environmental monitoring: Assessment of microbial community dynamics in various ecosystems.

Current Challenges

Despite significant advances, phageome research faces several challenges:

1. Dark matter: A large proportion of phage sequences in metagenomic datasets cannot be classified or characterized due to the lack of reference genomes.

2. Methodological limitations: Current techniques may exclude certain types of phages, such as single-stranded DNA (ssDNA) and RNA phages.

3. Host-phage interactions: Understanding the complex relationships between phages and their bacterial hosts in natural environments remains challenging.

As sequencing technologies and computational methods continue to improve, our understanding of phageomes and their ecological and biological significance is expected to expand significantly.