MHD10 Virus, fungi and archaea Flashcards
Why is a virus not classified as an organism?
because it is incapable of autonomous reproduction, growth or replication. It can only multiply after it has infected the living cell of a eukaryote or prokaryote.
What is a virion?
An intact, infectious virus particle
How many viruses are there on earth?
10^31
What is the size difference between bacteria and virus?
The majority of known viruses are 10–100 times smaller than bacteria (which are approximately 400-nm long), but giant viruses have recently been described that are larger than bacteria.
The majority of viruses on earth infect ______
Bacteria
What can giant viruses be infected by?
Viruses called virophages
What are the most abundant viruses on earth and the human body?
bacteriophages
What are the different steps of phage attachment?
landing attachment tail contraction penetration and unplugging DNA injection
What are the two types a phage can be?
can be lytic (virulent) or lysogenic (temperate)
What leads to increased diversification of viral species and is one of the ways bacteria develop increased resistance to antibiotics?
The ability of lysogenic bacteriophages to transfer genes from one prokaryotic host to another. Toxins and/or virulence factors can be shared among bacteria in the same way.
How can some phages alter the antigenicity of their hosts?
By producing enzymes that modify the O-antigen component of lipopolysaccharides of Gram-negative bacteria.
State the 4 steps of the lytic cycle
- Phage attaches to cell and injects DNA
- Phage DNA circularises and enters lytic cycle
- Phage takes over bacterial cell’s replication machinery to synthesis new DNA and proteins, and to assemble new virions
- Cell lyses releasing phages into surrounding environment
State the 4 steps of the lysogenic cycle
- Phage attaches to cell and injects DNA
- Phage DNA circularises and enters lysogenic cycle
- Phage DNA integrates into bacterial chromosome to become a prophage
- bacterium replicates normally
- Antibiotic treatment/environmental stressor can cause the phage genome to excise from the bacterial chromosome
What is the virome?
Comprises all the nucleic acids belonging to the virus-like particles (VLPs) associated with a particular ecosystem.
What makes up the human virome?
It is a genetically complex component of the microbiome, with the blood, nose, skin, conjunctiva, mouth, vagina, lungs and gastrointestinal tract harbouring their own distinct virus assemblages. Every healthy individual harbours a genetically unique virome predominated by double-stranded DNA from bacteriophages.
Why are viruses not easily isolated and propagated in the laboratory?
Either we do not know the hosts of specific viruses or cannot replicate conditions required for virus infection and propagation in vitro.
Why can transmission electron microscopy not be used to characterise viruses?
is not amenable to routine use in laboratories because of its expense and technical requirements, and its relatively high detection limit (105 VLPs)
What methods are used instead of TEM to characterise viruses?
PCR-based assays targeting specific viral genes for detection of viruses in samples.
Why are PCR assays of little to no use for virome analysis?
Viruses do not have universally conserved genes similar to the 16S or 18S rRNA genes used to characterise prokaryotes and fungi, respectively, in metataxonomic studies. Consequently, the only means we currently have to characterise the virome is metagenomics.
How can virome megenomics be done?
Either by separating VLPs from the rest of the microbiome (a messy, laborious process) or by sequencing and assembling all DNA in a sample and identifying which parts of the assembled DNA come from viruses
What is likely to be the choice of separating VLPs in the future?
sequencing and assembling all DNA in a sample and identifying which parts of the assembled DNA come from viruses
Where is the best characterised viorme found in humans?
In the faeces
When is the intestinal virome estabilised and what is it predominated by?
The intestinal virome is established soon after birth and is predominated by bacteriophages. To a much lesser extent, representatives of human-, plant-, amoebae- and animal-infecting viruses are found along the gastrointestinal tract and contribute to the human intestinal virome.
Does everybody have the same intestinal and oral virome?
No everyone’s, is unique. but some bacteriophages are shared among individuals, especially among individuals who live in the same house.
What phyla predominate the intestine and the mouth
Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria predominate
How many bacteriophages are present in the healthy gut phageome (HGP)?
155
What do HGP do?
They play a main role in maintaining and possibly restoring a perturbed microbiota
HGP represents what percentage of total gut bacteriophages?
Only about 4% of the total gut bacteriophage community of an individual
How many viruses are there on earth?
10^31
What factors can modulate the human intestinal virome
birth mode, age, diet, medication, immune status, lifestyle and environment
What is Dysbiosis?
Disruption of the composition and/or function of the gut microbiome relative to that of healthy individuals is sometimes referred to as dysbiosis.
What happens in dysbiosis?
The virome is associated with certain disease states and is characterised by changes in the diversity, and predominance of specific virotypes.
Describe 4 features of dysbiosis?
- Altered prokaryotic and phage populations
- Impaired Intestinal barrier (epithelial cells and mucin)
- Dysregulation activation of immune system
- Introduction of microbial components to host systems
Describe 4 features of homeostasis?
- Diverse microbiota
- Intact intestinal barrier (epithelial cells and mucin)
- Bacteriophage adherence to mucus model of protection
- Controlled activation of immune system
List how can viruses contribute to maintaining our health?
1) The ‘bacteriophage adherence to mucus’ model of protection
2) Protective stimulation of host innate immune system by viruses
3) Involvement in maturation of host (mammalian) cells
Explain how virus maintain human health by the ‘bacteriophage adherence to mucus’ model of protection
A large number of bacteriophages within the intestinal mucosa may protect the host from bacterial infections by limiting the presence of mucosal bacteria (i.e. the bacteriophages kill potential pathogens), providing non-host-derived immunity operating throughout the gastrointestinal tract
Explain how virus maintain human health by the protective stimulation of host innate immune system
All viruses and/or their proteins or nucleic acids can produce an immune response. This can be exploited to treat diseases such as cancer. By deliberately using bacteriophages that target tumours, you could promote anti-cancer immunity and treat the disease
Explain how virus maintain human health by the involvement in maturation of host (mammalian) cells
Germ-free mice do not have a microbiota. As a result, they have an immature immune system and abnormal organs. Once germ-free mice are provided with a complex gut microbiota (either by faecal microbiota transplantation or feeding them microbe-containing food), their immune system and organs begin to resemble those of healthy animals with an intact microbiota. Giving germ-free mice a Murine norovirus (positive strand RNA virus) replicates the beneficial effects that providing them with a full normal microbiota would, restoring small-intestinal morphology and lymphocyte function without overt inflammation or disease. In wild-type mice, suppressing the bacterial and archaeal components of the gut microbiota using antibiotics then giving the mice Murine norovirus for 10 days increases villi width, Paneth cell granules, intestinal T cells and IFN-γ expression, producing comparable results to when antibiotic-treated mice are inoculated with strains of commensal bacteria. This highlights the importance of the virome in normal animal development.
