The human virome: assembly, composition and host interactions

Abstract

The human body hosts vast microbial communities, termed the microbiome. Less well known is the fact that the human body also hosts vast numbers of different viruses, collectively termed the ‘virome’. Viruses are believed to be the most abundant and diverse biological entities on our planet, with an estimated 10 31 particles on Earth. The human virome is similarly vast and complex, consisting of approximately 10 13 particles per human individual, with great heterogeneity. In recent years, studies of the human virome using metagenomic sequencing and other methods have clarified aspects of human virome diversity at different body sites, the relationships to disease states and mechanisms of establishment of the human virome during early life. Despite increasing focus, it remains the case that the majority of sequence data in a typical virome study remain unidentified, highlighting the extent of unexplored viral ‘dark matter’. Nevertheless, it is now clear that viral community states can be associated with adverse outcomes for the human host, whereas other states are characteristic of health. In this Review, we provide an overview of research on the human virome and highlight outstanding recent studies that explore the assembly, composition and dynamics of the human virome as well as host–virome interactions in health and disease.

Viruses and Type 1 Diabetes: From Enteroviruses to the Virome

“…The early infant virome is directly influenced by breastfeeding [219], affecting phage distribution, with human-infecting viruses not typically detected prior to until 3-4 months of age. Mode of birth (vaginal vs. caesarean section) is also important, with infants born via vaginal delivery showing greater viral diversity; however these findings have been contradicted in a separate study [220][221][222]. Mother-to-infant transmission of the virome has been proposed from breast milk, supported by significant homology between bacteriophage sequences detected in breast milk and stool viromes [219,223,224].…”

“…Non-enveloped viruses are most frequently detected in human faeces due to their ability to survive the acidic stomach environment and dehydrating nature of the large intestine. Phages such as crAssphages (cross-assembly phage, member of Caudovirales ) and also members of Microviridae have been identified as the most abundant type of virus in the mature gut [ 220 , 232 , 233 ]. Given the limited early persistence of vertebrate-infecting viruses, it could be suggested any persistent infections or colonisations that occur may be important.…”

Viruses and Type 1 Diabetes: From Enteroviruses to the Virome

“…The early infant virome is directly influenced by breastfeeding [215], affecting phage distribution, with human-infecting viruses not typically detected prior to until 3-4 months of age. Mode of birth (vaginal vs caesarean section) is also important, with infants born via vaginal delivery showing greater viral diversity, however these findings have been contradicted in a separate study [216][217][218]. Mother-to-infant transmission of the virome has been proposed from breast milk, supported by significant homology between bacteriophage sequences detected in breast milk and stool viromes [215,219,220].…”

“…Non-enveloped viruses are most frequently detected in human faeces due to their ability to survive the acidic stomach environment and dehydrating nature of the large intestine. Phages such as crAssphages (cross-assembly phage, member of Caudovirales) and also members of Microviridae have been identified as the most abundant type of virus in the mature gut [216,228,229]. Given the limited early persistence of vertebrate-infecting viruses, it could be suggested any persistent infections or colonisations that occur may be important.…”

Machine Learning Uncovers Adverse Drug Effects on Intestinal Bacteria

“…Bacteria, fungi, viruses, and archaea inhabit every region of the GI tract, forming a dynamic and diverse genetic reservoir known as the gut microbiome [ 1 ]. Though the presence of gut microorganisms has been known for decades, the identities, functions, and scale of gut microbiota has only recently begun to be characterised [ 2 , 3 , 4 ]. It is now recognised that an individual’s gut microbiome is as unique as a fingerprint, with microbial composition constantly adapting to changes in diet, age, lifestyle, health, and medication use [ 5 , 6 , 7 , 8 , 9 , 10 ].…”