Lecture 3

Question 1

What are all viruses?

Answer 1

obligate intracellular parasites. they only grow (ie replicate) in appropriate host cells.

Question 2

what is a virion? how can they be seen?

Answer 2

the name given to a purified virus particle. can be seen using EM.

Question 3

what do phages infect?

Answer 3

bacteria and archaea.

Question 4

what is the structure of a virus?

Answer 4

all virus particles contain nucleic acid genome and capsid proteins; many are enveloped with membranes. Viral genomes can either be RNA or DNA, single or double stranded.

Question 5

are many genes shared between major groups of viruses?

Answer 5

few/no genes shared.

Question 6

how do you study viral diversity in the microbiota?

Answer 6

direct sequencing of viral genomes

Question 7

what is the human viriome?

Answer 7

the entire collection of viral genomes isolated from human tissues

Question 8

what is the common type of virus identified from human samples?

Answer 8

bacteriophages

Question 9

what are eukaryotic viruses derived from?

Answer 9

food- e.g. plant viruses- the most common RNA virus isolated from the digestive tract.

Question 10

what can eukaryotic viruses infect?

Answer 10

microbial eukaryotes (e.g. Giardia and Trichomonas), can modulate mucosal inflammation.
viruses infecting human cells: pathogenic viruses and potential mutualistic viruses.

Question 11

what is the most widely used phylogenic marker?

Answer 11

small submit ribosomal RNA (SSUrRNA) gene.

Question 12

what SSUrRNA gene is found in each life form?

Answer 12

16SrRNA in prokaryotes, 18SrRNA in eukaryotes and 12SrRNA in mitochondria and plasmids.

Question 13

why is SSUrRNA the most used phylogenic marker?

Answer 13

its functionally constant- part of the ribosome.
sufficiently conserved, allowing cloning with degenerate primers (PCR) and information alignments to profile taxonomic composition of microbiota.

Question 14

Why can’t SSUrRNA be used for viruses?

Answer 14

they have no ribosomes.

Question 15

what has SSUrRNA sequencing told us?

Answer 15

its revealed key features of microbial communities’ structure and microbial interactions.

Question 16

what is Metagenomics and the meta genome?

Answer 16

Metagenomics sequences an entire population, and the meta genome is a mix of microbial clones and species of a given habitat.

Question 17

what is the unit of study in Metagenomics?

Answer 17

the microbial community in a specific niche.

Question 18

what does genome sequencing look like in practice?

Answer 18

extract DNA from faecal material, fragment the genome, large scale random “shotgun” sequencing, >1 billion reads of ~300bp, complete genome sequences of >100 bacteria in one run.

Question 19

why can’t the majority of micro-organisms not be cultured?

Answer 19

they’re anaerobic for example Bacteroides.

Question 20

what can Metagenomics be used for in practice?

Answer 20

to see how the features of microbiota change between healthy and diseased states.

Question 21

what happens if you only focus on DNA in Metagenomics?

Answer 21

you’ll completely miss any RNA viruses.

Question 22

what were the goals of the human microbiome project?

Answer 22

• determening whether individuals share a core human microbiome.
• understanding whether changes in the human microbiome can be correlated with changes in human health.
• developing the new technological and bioinformatic tools needed to support these goals.
• addressing the ethical, legal and social implications raised by the human microbiome research.

Question 23

what are cross-sectional studies of the human microbiota?

Answer 23

observation of all members of a population, or a representative subset, at one specific point in time.

Question 24

what are longitudinal studies of the human microbiota?

Answer 24

studies that involve repeated observations of the same variables over long periods of time- often many decades, for example, how microbiome changes as we age.

Question 25

what are case-control studies of the microbiota?

Answer 25

observational study in two existing groups with different features are compared on the basis of some supported casual attribute. (e.g. healthy vs diseased state: smoker vs non-smoker, IBD vs healthy.)

Question 26

what % of the faecal material is made of bacteria and microbes?

Answer 26

60%

Question 27

why is the lowest amount of microorganisms in the stomach? and how do some microbes survive there?

Answer 27

due to the low stomach ph, some organisms survive by sticking under the mucosal surface.

Question 28

which mucosal surface has the greatest variety of microbiota?

Answer 28

the GIT is very distinct from the others.

Question 29

what are the major bacteria phyla in the gut?

Answer 29

Bacteroides and Firmicutes.

Question 30

what are CAZymes?

Answer 30

carbohydrate active enzymes

Question 31

what are the four major types of cazyme categories?

Answer 31

• Glycoside hydrolases (GH): 130 families.
• Polysaccharide lyase (LH): 22 families.
• Carbohydrate estherases (facilitate the activities of GH and LHs)
• Glycosyl transferases (not degrading).

Question 32

what kind of bacteria are Bacteroides and Firmicutes?

Answer 32

Bacteroides gram negative, firmicutes gram positive.

Question 33

what phyla of bacteria contain the most CAZymes?

Answer 33

Bacteroides and firmicutes.

Question 34

which phyla of bacteria evidently increases in dysbioitic states in the lung microbiome?

Answer 34

Proteobacteria

Question 35

what can SCFAs do?

Answer 35

they can dampen down inflammatory pathways in the gut macrophages and DCs, promoting the development of Treg cells and maintain gut epithelial integrity and health.

Question 36

in a mouse model, SCFAs were shown to do what?

Answer 36

circulating SCFAs can modulate the properties of DC leading to reduces Th2 proinflammatory responses in the lungs.