Human Virome

The human virome is the complete collection of viruses, including bacteriophages, found in and on the human body. It contains animal viruses such as Anelloviridae, commensal bacteriophages that regulate bacterial populations, and transient dietary and environmental viruses. The human body may harbor approximately 10¹³ viral particles, though abundance varies significantly by body site and detection method.

Virome composition is strongly body-site specific. The gastrointestinal tract hosts the densest virome with approximately 10⁹–10¹⁰ virus-like particles per gram of feces, dominated by bacteriophages. The oral cavity and respiratory tract contain both phages and eukaryotic viruses including Herpesviridae and Adenoviridae. Cerebrospinal fluid is normally sterile, though trace viral nucleic acids have occasionally been detected.

Newborns typically acquire viruses from their surroundings and bacteriophages associated with bacteria that first colonize their bodies. Factors such as mode of delivery, breastfeeding, diet, and geographical location shape both the early-life virome and the adult virome. Viral colonization begins soon after birth through prophage induction from early bacterial colonizers and environmental exposure.

Although virome composition tends to remain relatively stable within the same individual over time, it can be disrupted by infection, antibiotic use, major dietary changes, or immunosuppression. These factors alter the balance of viral populations and can lead to changes in both bacteriophage and eukaryotic virus abundance throughout the body.

Most detected human-associated viruses are bacteriophages, particularly members of the Caudovirales and Microviridae families. Many eukaryotic viruses identified in healthy individuals, including Anelloviridae and Redondoviridae, persist without causing overt disease. Their increased abundance in immunocompromised hosts suggests that host immunity plays a role in regulating viral load.

Comprehensive characterization of the virome became possible only with untargeted shotgun metagenomic sequencing, which revealed extensive viral diversity and a large fraction of genetically unclassified sequences termed viral dark matter. This technology has enabled researchers to detect viruses that were previously unidentifiable and understand the true complexity of viral communities across different body sites.

Altered virome patterns have been linked to conditions such as inflammatory bowel disease, type 1 diabetes, and colorectal cancer, although causal relationships have not been established. Beyond direct pathogenic effects, the virome influences host health indirectly by shaping bacterial communities, facilitating gene transfer, and modulating immune signaling throughout the body.