Human Virome: Composition and Diversity

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Questions and Answers

What is the relationship between the establishment of the virome and the microbiome in neonates?

The establishment of the virome in neonates is closely linked to the timing of microbiome colonization as both develop simultaneously after birth.

What evidence suggests that neonates are initially sterile?

Historically, the inability to culture microorganisms from healthy deliveries suggested that neonates were born sterile.

What role do lysogenic phages play in the gut virome during the first month of life?

Lysogenic phages play a significant role in the gut virome of infants, as ongoing lytic phage replication was not detected in direct infection assays.

Why are Microviridae and crAssphages considered rare during the first month of an infant's life?

Microviridae and crAssphages are rare or absent in the infant gut during the first month because they typically do not form lysogens. Signup and view all the answers

What findings did recent studies unveil about bacterial strains isolated from infants?

Recent studies found that many bacterial strains isolated from infants' stools produced viral particles at high levels. Signup and view all the answers

What is the significance of the term 'dark matter' in the context of viral sequencing?

'Dark matter' sequences refer to unannotated viral sequences that contribute significantly to the understanding of the virome. Signup and view all the answers

How do technical mishaps affect the understanding of viral colonization?

Technical mishaps associated with reagent contamination can complicate the clarity of how much colonization is attributed to viral replication versus contamination. Signup and view all the answers

What was concluded about lytic phages in infant gut samples from the recent study?

The recent study concluded that lytic phages were relatively rare in infant gut samples during the first month of life. Signup and view all the answers

What is the primary purpose of filtration in the context of purifying viral-like particles (VLPs)?

The primary purpose of filtration is to separate and purify VLPs by exploiting the size differences between viruses and larger particles. Signup and view all the answers

What pore sizes are commonly used in filters for purifying VLPs?

Commonly used filter pore sizes include 0.2 μm and 0.45 μm. Signup and view all the answers

What is one potential disadvantage of using a 0.2-μm filter in the filtration process?

Using a 0.2-μm filter may result in the loss of larger viruses that cannot pass through the filter. Signup and view all the answers

How does the stability of RNA viruses in metagenomic samples affect studies on these viruses?

RNA viruses are generally less stable in samples typically used for metagenomics, which can lead to undersampling of these viruses. Signup and view all the answers

According to studies, how many species were predicted to be phages in the virome?

Approximately 32,000 species were predicted to be phages. Signup and view all the answers

Why is it important to establish viral taxa in virome studies?

Establishing viral taxa is critical as it helps in understanding the diversity and ecological roles of viruses within the virome. Signup and view all the answers

What challenge arises from the inability to grow certain Anelloviridae in pure culture?

The inability to grow certain Anelloviridae hinders the understanding of their biology and role in the virome. Signup and view all the answers

Why are viral lineages now commonly specified by sequences rather than successful culture?

Viral lineages are specified by sequences because many members of the virome cannot be cultured successfully in vitro. Signup and view all the answers

What are temperate phages and how do they replicate?

Temperate phages are viruses that can replicate via both lytic and lysogenic pathways. Signup and view all the answers

Explain pseudolysogeny and its significance in phage survival.

Pseudolysogeny is a state where phage genomes exist as episomes without integrating into the host genome, enabling phages to persist without killing the host. Signup and view all the answers

Identify two types of viruses that may establish long-term latency in humans.

Torque teno virus and torque teno mini virus are examples of viruses that can establish long-term latency in human cells. Signup and view all the answers

What role do commensal viruses play in the human virome?

Commensal viruses act as benign colonizers in the human virome and are not associated with any particular disease. Signup and view all the answers

How do viruses that bud out of infected cells differ from lytic phages?

Viruses that bud out of infected cells do not cause cell lysis and death, allowing the host cell to survive. Signup and view all the answers

What is the primary method used to study the virome?

Isolating virus-like particles (VLPs) from samples is the primary method for studying the virome. Signup and view all the answers

Describe the significance of the Gut Virome Database (GVD).

The Gut Virome Database (GVD) is significant as it provides a regularly updated repository of virome-derived contig databases. Signup and view all the answers

What structural feature characterizes the Anelloviridae family of viruses?

The Anelloviridae family is characterized by its non-enveloped, single-stranded DNA with small circular genomes. Signup and view all the answers

Study Notes

Human Virome: Composition and Host Interactions

The human body is colonized by a vast community of viruses, collectively termed the virome.
The virome is estimated to contain approximately 10¹³ particles per individual, with considerable heterogeneity.
Virus-like particles (VLPs) are often abundant in environmental samples and human fecal matter, but replication competence is uncertain for many of these.
Metagenomic sequencing highlights the diversity of the human virome, revealing many unidentified viral "dark matter" sequences.
Different body sites have distinct virome compositions, with the gut harboring the most abundant populations.

Human Virome Diversity

The number of viruses in the human body is comparable to the number of human and bacterial cells (approximately 10¹³).
Viruses are categorized by their genetic material (RNA or DNA), strandedness (single- or double-stranded), and genome size.
Viral particles have protein coats (capsids) and may have lipid membranes.
Morphological classifications include spherical (icosahedral), filamentous, bullet-shaped, and tailed (for phages).

Virome and Disease

Many studies link specific virome profiles to certain diseases. Examples include alterations in the virome in Crohn's disease, ulcerative colitis, type 1 diabetes, and colorectal cancer.
Generally, more research is needed to establish causal relationships between virome alterations and disease.
The virome composition may correlate with disease outcomes.
Understanding the virome's role in inflammatory bowel disease, diabetes, hypertension, and cancer is an active area of research.

Virome Assembly in Early Life

Neonates typically lack a detectable virome at birth, but are quickly colonized after birth.
Phage induction by pioneering bacteria may contribute to the initial virome population shortly after birth.
The virome continues to evolve during early life.
Factors like diet (e.g., breastfeeding) and birth mode (e.g., vaginal delivery vs. Cesarean section) may influence virome assembly and composition.

Factors Influencing the Human Virome

Diet, specifically breastfeeding, is linked to virome composition, potentially decreasing viral load.
Genetics plays a role in virome profiles
Cohabitation, geographical location, age, and the presence of disease are also determinants of virome diversity.

Methods for Virome Study

Methods to study the virome include: isolating virions from samples, filtering to separate the virions from other elements, viral population analysis through shotgun sequencing, and VLP purification.
Contamination with environmental DNA is a challenge requiring multiple blank sample analyses for quality control.
Abundant software for analyzing the data generated by metagenomic sequencing is available to researchers.

Human Virome in different Body Sites

The oral cavity, nervous system, gastrointestinal tract, urinary, respiratory, skin, and urogenital system viromes are diverse.
Viral populations are not uniformly distributed throughout the body.
The composition of viromes in different body sites is often specific to that site.
Viral localization in different body sites often correlate with variations in the composition of the microbial community in that area

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Description

This quiz explores the vast community of viruses known as the human virome. It delves into its composition, diversity across different body sites, and the implications of metagenomic sequencing in understanding these viral populations. Test your knowledge on the intricate relationships between viruses and their human hosts.