Lecture 5

Question 1

what are glycans?

Answer 1

an umbrella term for polysaccharides, oligosaccharides and glycoconjugates, e.g. glycoproteins).

Question 2

what produces butyrate, propionate and acetate?

Answer 2

butyrate- mainly Firmicutes
propionate- mainly Bacteroidetes
acetate- most gut bacteria

Question 3

what do all 3 SCFAs stimulate?

Answer 3

anti-inflammatory pathways.

Question 4

what does butyrate do?

Answer 4

its a main energy source of colonocytes.

anti-cancer, suppress cancer cell proliferation and induces apoptotic cell death.

Question 5

what does propionate do?

Answer 5

maintains glucose homeostasis.

reduces apetite- means we don’t eat too much.

Question 6

what does acetate do?

Answer 6

prevents colonisation by some pathogens (lowers ph)
increases butyrate production (x-feeding)
affects lipogenesis.

Question 7

what is evidence that SCFAs are used by our bodies?

Answer 7

only 5% of the SCFAs made are found within the faeces.

Question 8

what is IBD characterised by?

Answer 8

chronic inflammation- has genetic and dietary component.

Question 9

what is a possible explanation of why ulcerative colitis is often found in the distal colon and rectum.

Answer 9

there’s lower levels of SCFA in the descending colon so SCFAs not dampening down inflammation here leading to UC.

Question 10

why does the colon have a thick layer of mucus?

Answer 10

to protect underlying epithelial cells from infiltration by microbiota and pathogens. if infiltration occurs we get excess inflammation.

Question 11

what is the mucus layer in the colon like?

Answer 11

transit slows down and microbe loads increase dramatically, there’s 2 discrete layers of mucus, a more sterile impenetrable layer which is surrounded by an outer layer.

Question 12

in a study with germ-free mice, what happened when the mice were given a human microbiome and fed a low-fibre diet?

Answer 12

the microbes which were known to feed on mucin increased in population.

Question 13

what happens when the mucin degrading bacterial population increases?

Answer 13

the mucus barrier gets finely degraded, pathogen can get across the barrier and cause disease.
chronic inflammation can be caused if microbial products or even intact bacteria translocate from the intestine into the systemic circulation.
barrier becomes dysfunctional.

Question 14

so what re the two ways glycol metabolism is important for gut health?

Answer 14

production of SCFAs, protection of mucus barrier.

Question 15

who are the main players in glycol breakdown in the gut?

Answer 15

Bacteroidetes are generalists, Firmicutes and Actinobacteria also play a significant role but are much more specialised.
Bacteroidetes have a wide range of glycans they can digest.

Question 16

two common gut Bacteroides species were isolated from the gut, what could they break down?

Answer 16

they had distinct glycans they could break down, but together they could break down pretty much everything.

Question 17

What were the preferences of B. ovatus and B. theta?

Answer 17

Ovatus likes plant polysaccharide, theta likes mucin glycan.

Question 18

what is PULs and what do they encode?

Answer 18

Polysaccharide utilisation loci, they encodes us-like systems.

Question 19

what is a sus-like system?

Answer 19

Starch utilisation system, because first characterised targeted starch, but each sus-like system targets a different glycan.

Question 20

What ares sus-like systems unique to?

Answer 20

Bacteroidetes.

Question 21

How many PULs does Bt have?

Answer 21

88

Question 22

what are PULs defined by?

Answer 22

homologues of susC/D as well as the presence of glycoside hydrolase genes + normally linked to sensor-regulator.

Question 23

why do Bacteroidetes need sus-like systems?

Answer 23

they’re gram negative so require this system to get things across the membrane for it to be broken down further.

Question 24

how do you know which PUL targets which glycan?

Answer 24

using transcriptomics of Bt and Bo growth on purified polysaccharide showed which PUL was activated in the presence of which polysaccharide.

Question 25

what are susC and susD?

Answer 25

susC is a transmembrane channel with susD associated with it.

Question 26

what is susD required for?

Answer 26

susD binds target glycan with low affinity and is required for oligosaccharides larger than 5 sugars.
suggests role of susD is to deliver larger oligos to susC transporter but it is not known how.

Question 27

how do we know that susD is important for oligosaccharides with more than 5 sugars?

Answer 27

when susD was knocked out, there was no effect on smaller sugars, but over 5 sugars the pore could no ,longer import larger sugars.

Question 28

what was recently discovered about the susCD structure?

Answer 28

susD sits on susC like a lid.

Question 29

what happens to susCD when a ligand is present and absent?

Answer 29

when ligand present, susD closes to keep the ligand within the structure, when ligand is absent, sus D opens to allow ligand in.

Question 30

what is susE?

Answer 30

it is part of CD complex on surface (lipoprotein)

Question 31

what’s the role of susE?

Answer 31

it binds glycans with a high affinity. its often called surface glycan binding protein (SGBP).

Question 32

what happens if you knock out susE from the starch PUL?

Answer 32

The SGBP gene knockout shows no growth defect on starch, but a defect appears if the knockout has to compete against WT.
it suggests that the role of SGBP is in glycan capture, and it provides a competitive advantage in a densely populated gut.

Question 33

why do almost all sus-like systems have surface located endo acting glycanase enzyme?

Answer 33

there’s a size-limit for import by susCD- need surface enzyme to digest long polysaccharides to oligosaccharides.

Question 34

how is glycan degradation by firmicutes different?

Answer 34

firmicutes generally have lower numbers of GHs and PLs than Bacteroidetes, which suggests that they’re more specialised.
firmicutes are gram positive, so no outermsmbrane to cross- just a thick peptidoglycan layer instead.

Question 35

what transporters do firmicutes have instead of susCD?

Answer 35

ABC transporters.

Question 36

what are ABC transporters?

Answer 36

cell wall anchored glyconases with lots of carbohydrate binding molecules to attach to substrate.

Question 37

what are some firmicutes (especially Ruminococci) associated with?

Answer 37

insoluble fibre particles in faecal samples.

Question 38

what are Bacteroidetes associated with more?

Answer 38

the liquid phase (soluble poly and oligosaccharides.)

Question 39

what are Bifidobacteria?

Answer 39

Actinobacteria gram positive.

Question 40

how do bifidobacterias break down glycans?

Answer 40

they use similar apparatus to firmicutes, ABC transporters and surface enzymes (GH), enzymes are less complex than in firmicutes. maybe because Bifidobacteria prefers to use oligosaccharides rather than the insoluble molecules firmicutes target.