The human body harbors a vast and diverse viral community known as the human virome. The virome includes bacteriophages that infect bacteria, and eukaryotic viruses that infect human cells. Transient dietary and environmental viruses also contribute to this dynamic ecosystem. Estimates suggest the human body may contain on the order of 10¹³ viral particles, though abundance varies widely by body site and detection method.
Comprehensive characterization of the virome has become possible only with untargeted shotgun metagenomic sequencing, which has revealed extensive viral diversity and a large fraction of genetically unclassified sequences termed viral dark matter. Although virome composition differs greatly between individuals, it tends to remain relatively stable within the same individual over time, unless disrupted by factors such as infection, antibiotic use, major dietary changes, or immunosuppression.
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, appear to persist without causing overt disease. Their increased abundance in immunocompromised hosts suggests a role for host immunity in regulating viral load.
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 in some studies, dominated by bacteriophages such as crAssphages. The oral cavity and respiratory tract contain both phages and eukaryotic viruses, including Herpesviridae and Adenoviridae. Viral envelopes are uncommon in fecal samples due to selective pressures of the intestinal environment. Low levels of viral nucleic acids have also been detected in blood and cerebrospinal fluid, though interpretation requires caution because of potential contamination.
Healthy neonates are generally thought to be born with minimal detectable virome. Viral colonization begins soon after birth through prophage induction from early bacterial colonizers and environmental exposure, with eukaryotic viruses becoming more prominent during infancy. Beyond direct pathogenic effects, the virome influences host health indirectly by shaping bacterial communities, gene transfer, and immune signaling. As sequencing technologies advance, understanding the human virome will be increasingly important for microbiome-based diagnostics and therapeutic strategies.
The human virome refers to the complete collection of viruses, including bacteriophages, found in and on the human body.
Many animal viruses, such as those from the family Anelloviridae, and commensal bacteriophages that regulate bacterial populations within the host microbiome are commonly found in healthy individuals.
The composition of the virome varies significantly across different body sites.
The gastrointestinal tract is the most abundant site for viral colonization.
In contrast, cerebrospinal fluid is normally sterile, although sensitive molecular techniques have occasionally detected trace viral nucleic acids with unclear biological significance.
Newborns typically acquire viruses from their surroundings and bacteriophages associated with the bacteria that first colonize their bodies.
Additionally, factors such as the mode of delivery, breastfeeding, diet, and geographical location shape both the early-life virome and the adult virome.
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.
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