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MHD10 Virus, fungi and archaea Flashcards

1
Q

Why is a virus not classified as an organism?

A

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.

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2
Q

What is a virion?

A

An intact, infectious virus particle

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3
Q

How many viruses are there on earth?

A

10^31

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4
Q

What is the size difference between bacteria and virus?

A

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.

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5
Q

The majority of viruses on earth infect ______

A

Bacteria

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6
Q

What can giant viruses be infected by?

A

Viruses called virophages

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7
Q

What are the most abundant viruses on earth and the human body?

A

bacteriophages

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8
Q

What are the different steps of phage attachment?

A 
landing
attachment
tail contraction
penetration and unplugging
DNA injection
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9
Q

What are the two types a phage can be?

A

can be lytic (virulent) or lysogenic (temperate)

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10
Q

What leads to increased diversification of viral species and is one of the ways bacteria develop increased resistance to antibiotics?

A

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.

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11
Q

How can some phages alter the antigenicity of their hosts?

A

By producing enzymes that modify the O-antigen component of lipopolysaccharides of Gram-negative bacteria.

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12
Q

State the 4 steps of the lytic cycle

A
  1. Phage attaches to cell and injects DNA
  2. Phage DNA circularises and enters lytic cycle
  3. Phage takes over bacterial cell’s replication machinery to synthesis new DNA and proteins, and to assemble new virions
  4. Cell lyses releasing phages into surrounding environment
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13
Q

State the 4 steps of the lysogenic cycle

A
  1. Phage attaches to cell and injects DNA
  2. Phage DNA circularises and enters lysogenic cycle
  3. Phage DNA integrates into bacterial chromosome to become a prophage
  4. bacterium replicates normally
  5. Antibiotic treatment/environmental stressor can cause the phage genome to excise from the bacterial chromosome
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14
Q

What is the virome?

A

Comprises all the nucleic acids belonging to the virus-like particles (VLPs) associated with a particular ecosystem.

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15
Q

What makes up the human virome?

A

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.

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16
Q

Why are viruses not easily isolated and propagated in the laboratory?

A

Either we do not know the hosts of specific viruses or cannot replicate conditions required for virus infection and propagation in vitro.

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17
Q

Why can transmission electron microscopy not be used to characterise viruses?

A

is not amenable to routine use in laboratories because of its expense and technical requirements, and its relatively high detection limit (105 VLPs)

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18
Q

What methods are used instead of TEM to characterise viruses?

A

PCR-based assays targeting specific viral genes for detection of viruses in samples.

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19
Q

Why are PCR assays of little to no use for virome analysis?

A

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.

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20
Q

How can virome megenomics be done?

A

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

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21
Q

What is likely to be the choice of separating VLPs in the future?

A

sequencing and assembling all DNA in a sample and identifying which parts of the assembled DNA come from viruses

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22
Q

Where is the best characterised viorme found in humans?

A

In the faeces

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23
Q

When is the intestinal virome estabilised and what is it predominated by?

A

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.

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24
Q

Does everybody have the same intestinal and oral virome?

A

No everyone’s, is unique. but some bacteriophages are shared among individuals, especially among individuals who live in the same house.

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25
What phyla predominate the intestine and the mouth
Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria predominate
26
How many bacteriophages are present in the healthy gut phageome (HGP)?
155
27
What do HGP do?
They play a main role in maintaining and possibly restoring a perturbed microbiota
28
HGP represents what percentage of total gut bacteriophages?
Only about 4% of the total gut bacteriophage community of an individual
29
How many viruses are there on earth?
10^31
30
What factors can modulate the human intestinal virome
birth mode, age, diet, medication, immune status, lifestyle and environment
31
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.
32
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.
33
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
34
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
35
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
36
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
37
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
38
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.
39
What is a bacteriophage?
A virus that infects and replicates within bacteria and archaea
40
The fungal component of the human microbiome is called what?
Mycobiome
41
Define: Mycology Medical mycology Mycosis (plural mycoses)
Mycology – the science and study of fungi Medical mycology – the study of fungi that produce disease in humans and other animals, and of the diseases they produce, their ecology and their epidemiology Mycosis (plural mycoses) – any disease caused by fungi
42
What are fungi cell walls made?
Chitin, glucans, mannans, glycoproteins
43
What within fungi walls causes an immune response in humans?
Chitin
44
Where is candida found?
skin, scalp, vagina and gut
45
When may canadida pose a threat?
Host health unless the body’s immune system is compromised or an individual has an underlying condition (such as diabetes mellitus) or is debilitated. In these susceptible individuals, Candida can cause various types of candidiasis
46
How many species of fungi are there on earth?
1.5 million species of fungus on Earth, but only 70,000 or so have been formally identified.
47
Are fungi pathogenic?
Of the known fungi, only 300 species cause disease in man, with the majority causing rare diseases in immunocompromised patients. Only a small number are common pathogens that cause disease in otherwise healthy humans.
48
Why are humans not easily infected by fungi?
Complex immune system and endothermy. Our body temperature is 37°C, which is too warm a temperature for most fungi to replicate & effective immune system
49
When fungal infections do occur in otherwise healthy humans they are _______
mild and self-limiting
50
What are 6 host defences against fungi?
- the fatty acids present in the skin - the pH of the skin - mucosal surfaces and body fluids - the turnover and shedding of cells preventing colonization of tissues (i.e. epithelial turnover) - the normal microbiota of the body preventing overgrowth of fungi and - the defences of the respiratory system
51
What does chronic inflammation seen in fungal diseases lead to?
destruction of tissue and fibrosis, leading to breathing difficulties and a debilitating disease known as extrinsic allergic alveolitis (which is inflammation of the alveoli).
52
How can fungi act as opportunistic pathogens?
In the immunocompromised or debilitated
53
How are fungi classified?
Fungi are divided based on their life cycles. That is, what their fruiting bodies look like and the arrangement of their spores.
54
What are the three major groups of fungi?
The moulds The mushrooms The microscopic yeasts
55
Multi-cellular filamentous fungi is an example of what group of fungi?
Moulds
56
Why are multi-cellular filamentous fungi and single-celled microscopic yeasts relevant to clinical and microbiome research?
We are constantly exposed to their spores via our diet (e.g. Saccharomyces cerevisiae, the fungus commonly used in baker’s yeast) and the environment.
57
What do filamentous fungi make up?
Hyphae
58
What do hyphae branch along surfaces to form?
Compact mats of growth called a mycelium
59
What helps fungi to spread and replicate?
The hyphae can grow upwards to form the fruiting bodies of the fungus in some species. The spores are released by the fungus so that they can be carried to a new environment through the air or in fluids. The spores can then germinate in a new suitable environment and start the life cycle over again.
60
What fungi are found primarily on rotting wood?
Aspergillus fumigatus
61
On average how many A. fumigatus spores do humans inhale everyday?
200
62
In healthy humans, what defends us against Aspergillus fumigatus?
Innate immune system (particularly alveolar macrophages)
63
In immunocompromised patients, what does A. fumigatus cause?
Chronic Pulmonary aspergillosis (a form of pneumonia particularly problematic for organ-transplant patients) and invasive aspergillosis (a life-threatening systemic infection involving the whole body)
64
What is the mortality rate associated with A. fumigatus infections
80%
65
What is the unicellular fungi that reproduces asexually and is of clinical relevance?
Yeast
66
How do yeast asexually reproduce?
by forming blastoconidia – that is, they undergo budding – or they reproduce by fission – that is, they split in two
67
The majority of fungal infections in humans are ______________
superficial infections
68
How are fungal infections transmitted?
Through person-to-person or animal-to-human spread. In these kinds of infections, fungi grow on the outermost layer of body surfaces: that is, the skin, hair, vaginal, mouth and mucosal surfaces.
69
What are the main superficial diseases caused by fungi?
are skin diseases caused by the dermatophytes, which include Microsporum, Epidermophyton and Trichophyton spp. (Don’t worry, you don’t need to remember these Latin names!) These three genera comprise 40 different species of fungus.
70
What do tinea/ringworm refer to?
skin fungal infections, tinea can also affect the hair and nails
71
How do tinea infections grow?
Moist environments and they have a characteristic appearance of raised red rings with a central area of clearing
72
Other than superficial infections, what type of infections can fungi cause?
- subcutaneous infections - nosocomial (hospital-acquired) infections - systemic infections - deep-seated infections
73
What do the types of tinea include?
Tinea barbae Tinea pedis Tinea manuum Tinea capitis
74
When do subcutaneous infections occur?
where the layers under the skin surface are infected and occur following skin penetration
75
Give an example of how nosocomial (hospital-acquired) infections occur?
IV lines are a route of entry for fungi
76
What is the problem with antifungal treatment?
Its toxic to human cells
77
Deep seated infections and systemic infections can lead to _______
organ failure
78
What are the two fungi that cause the highest number of opportunistic infections
Aspergillus and Candida
79
Allergic bronchopulmonary aspergillosis and Aspergillus sinusitis is caused by what?
An allergic response to Aspergillus antigens which causes inflammation in the lungs or sinuses
80
How can Cutaneous aspergillosis occur?
f there is a break in the skin or if invasive aspergillosis spreads to the skin
81
When do Candida infections cause thrush?
If they infect mucus membranes
82
When does invasive candidiasis occurs?
When Candida enters the bloodstream and is associated with hospital-associated interventions
83
Are archaea prokaryotes or eukaryotes?
Prokaryotes
84
What are archaea cell membranes made of?
High levels of glycerol-ether (rather than glycerol-ester) lipids that are hard to break open.
85
Why are archaea under-represented in DNA-based microbiome studies?
Due to their hard-to-break cell membranes
86
What is the name of methane producing archaea?
Methanogens
87
What do Methanogens generate methane from?
simple substrates that tend to be the end-products of bacterial catabolism (CO2, H2, formate, trimethylamine, and methanol)
88
The abundance of methanogenic archaea________from the ascending to the descending colon and from childhood into adulthood
increases
89
What are hydrogenotropic methanogens?
They use H2 to reduce CO2 and methyl components. and are the most commonly detected archaea in the gut.
90
What order do hydrogenotropic methanogens belong?
Methanobacteriales
91
What is the role of hydrogenotropic methanogens
They reduce the partial pressure of the gut by reducing CO2 whilst using H2
92
What is the name of a type of methylotrophic archaea that utilise one carbon compound?
Methanomassiliicoccales
93
What is the most prevalent archaeon in the gut?
Methanobrevibacter smithii
94
What is the function of Methanobrevibacter smithii?
It reduces CO2 to CH4 using H2 as the primary electron donor. It can also utilise formate to directly produce CH4. It participates in non-methanogenic removal of bacterial end-products as well, by using ammonium, ammonia, nitrogen sources and ethanol.
95
What is Methanobrevibacter smithii's colonisation of the intestine is facilitated by?
Its cell surface being covered in glycans, which mimic those found in the intestinal mucosa.
96
Methanomassilicoccus luminyensis is another methanogen which can use ________ or _____as an electron acceptor to produce methane
methanol or TMA
97
Methanomassilicoccus luminyensis's ability to remove TMA from the gut has led to the suggestion of utilising it as a probiotic for individuals with which type of disease?
Individuals with fish odour syndrome or at risk of CVD

Microbiome (10 decks)

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