Lecture 2

Question 1

How can bacterial store their genomic information?

Answer 1

Mostly circular, but occasionally, linear chromosomes and plasmids.

Bacteria can have one or multiple chomosomes.

Question 2

What range of bacterial genome sizes exist?

Answer 2

0.14Mb to 14.3Mb

Question 3

What usually underpins bacteria having larger genomes?

Answer 3

Needing more genes because you live in more complex environments

Question 4

What is the common bacterial genome size?

Answer 4

Between 2 and 6Mb

Question 5

How do bacterial genomes acquire new genes?

Answer 5

Genes that are remnants of phage attack can be found in bacterial genomes

Bacteria will naturally take up DNA form their environment (are transformable)

Question 6

What is the core genome?

Answer 6

Core genome - Genes that are seen in all strains of the species

Question 7

What is the dispensable genome?

Answer 7

Genes that are present in two or more strains

Question 8

What are unique genes?

Answer 8

Genes that are specific to an individual strain

Question 9

What is the pan-genome?

Answer 9

The pan-genome is the full complement of genes in a clade.

Made up of the core genome, dispensable genome and unique genes.

Question 10

What is reductive evolution?

Answer 10

Loss of genes that are no longer required

e.g. Evolution of extracellular bacteria that have become intracellular; in which they lose genes that are now superfluous in their new environment.

Question 11

What are pseudogenes?

Answer 11

Genes which have lost their ability to be expressed; an outcome of reductive evolution

Question 12

What can cause rapid emergence of genetically uniform pathogens form variable ancestors?

Answer 12

Genetic bottlenecking

Individuals acquire new trait which makes them more likely to survive. Outcompete other individuals untill only pathogen with that trait surviving

Question 13

Why are the genomes of pathogenic bacteria commonly smaller than non-pathogenic bacteria?

Answer 13

Narrower functional range

Question 14

What stages does a bacteria go through from being free-living and extra-cellular to being an organelle?

Answer 14

From free-living and extracellular to facultative intracellular, to obligate intracellular, to obligate intracellular mutualist, to organelle.

Question 15

Where do enteric pathogens live?

Answer 15

In the gut

Question 16

Where are the potential carbon sources in the gut?

Answer 16

Host glycans on mucin proteins

From the digested food

Question 17

How are host sugars taken up by enteric pathogens?

Answer 17

Anaerobic residents in the lower bowel digest polysaccharides and liberate free sugars. These monosaccharides can then be used by the enteric pathogens. Some enteric pathogens can’t use the polysaccharides.

Question 18

What has been shown about the sugar comsumption of commensal and pathogenic E.coli?

Answer 18

Both are very flexible and can use a wide range of carbon sources. But commensal (MG1655) and pathogenic (EDL933) have differential use of these C-sources. With preferences about which order they use them in.

Question 19

What will E.coli use as a carbon source last?

Answer 19

After all sugar has run out the E.coli will use acetate

Question 20

Which sugars were shown to be more timportant to the EDL strain than the MG strain?

How?

Answer 20

Galactose and Mannose

Knockout mutants of EDL strain for catabolism gene of each sugar grew less in mouse model then wild type. Effect not as large in MG strain.

Question 21

Which sugar was shown to be more important to MG strain?

Answer 21

Sialic acid

Question 22

What effect does secondary infection with a commensal strain have on a mouse already infected with a different commensal strain?

Answer 22

The numbers of the first strain slightly decrease but stay high, the numbers of the second strain increase to match that of the first strain. The two can have different niches; and not effect each other.

Question 23

What effect does secondary infection with a commensal strain have on a mouse already infected with a pathogenic strain?

Answer 23

The pathogenic strain is unable to accumulate and the numbers decrease soon after infection - therefore the commensal strain appears to protect the mouse.

Question 24

What is the function of the VPI-2 in vibrio cholerae?

Answer 24

Conatains a series of metabolic genes which can release sialic acid from host proteins and consume it.

NanH encodes a sialidase which can cleave sialic acid from host mucin proteins

Question 25

Which gene from the VPI-2 has been shown to be important in earrly colonisation of mouse models?

Answer 25

The nanA gene

Loss of the gene by deletion causes a signicant decrease in the number of CFU’s in early colonisation

Question 26

What effect can anti-biotic treatment sometimes have?

Answer 26

Removes infection by initial bacteria however can cause infection from other bacteria due to loss of microbiota and hence more space and more nutirents for the enteric pathogens to grow in. E.g. clostridium difficile

Question 27

What was the initial hypothesis of the Sonnenburg paper?

Answer 27

Post-antibiotic treatment the microbiota that usually comsume the free monosaccharides from mucin proteins are gone. Therefore the pathogenic bacteria, C.difficle and salmonella trphimurium, have more esy access to the monosaccharides.

Question 28

What is a gnotobiotic mouse?

Why are they useful?

Answer 28

A mouse with no microbiota. Breed under controlled conditions.

Can add single organisms that you are interested in with no interference. Similar conditions to those seen in anti-boitic treated individuals.

Question 29

How did Sonnenburg use gnotobiotic mice to identify salmonella genes?

Answer 29

Mice were monoassociated with Bacteriodes thetatiotaomicron, to model a microbiota that is susceptible to pathogenic emergence. Model and germ-free mice were give S. typhimurium and then the caecal contents were collected five days later and sujected to transcriptional profiling using a S.typhimurium gene chip.

Question 30

What did the gene chip show about salmonella gene expression?

Answer 30

Genes expression of nan, fuc and pdu operons were higher in Bacteriodes thetatiotaomicron infected mice then in germ-free mice and in-vitro studies. Nan operon for sialic acid transport and catabolism. Fuc and pdu operons for fucose transport and catabolism.

Question 31

How were these increases gene expression checked?

Answer 31

qRT-PCR of in vitro results of germ-free free and Bacteriodes thetatiotaomicron pre-treated culture

Question 32

What effect did loss of nanA and fucI have on the salmonella growth?

Answer 32

Resulting strains cannot grow on either as thier sole carbon source

Question 33

What was shown by the competition index of effect of Bt on growth of nanAfacI salmonella mutants?

Answer 33

nanAfucI mutant has significatn disadvantged to the wild type on days 1&2 after infection when Bt is present but not when Bt is absent

Question 34

What efect does Bt have on sialic acid?

How was this seen in the paper?

Answer 34

Bt has a sialidase to cleave the sialic acid but no catabolic genes to catabolise it.

In presence of Bt there was an increase of sialic acid in caecal matter, this was not seen when mutant of Bt lacking it sialidase activity was used.

Question 35

What does the paper argue the Bt cleaves the sialic acid for if its not going to catabolise it?

Answer 35

Release of the sialic acid allows the Bt to access the carbohydrates it is actually interested in which lie below the sialic acid.

No evidence of this claim

Question 36

What effect was Bt infection shown to have of C.difficile?

Answer 36

Increased expression of nan genes and more CFU’s.