Intro To Microbiology Of The Gut

Question 1

What is the microbiome?

Answer 1

Collection of bacteria, archea, fungi, Protozoa and viruses that colonise our body surface and their respective genomes and metabolic activities

Question 2

What are the main bacterial phyla in the gut?

Answer 2

Firmicutes, bacteroidetes, actinobacteria and proteobacteria

Question 3

What is the ratio of human cells: bacterial cells in the body?

Answer 3

1:1

Question 4

What is a resident flora?

Answer 4

Your flora thats with you for life

Question 5

What is the difference between transient and resident flora?

Answer 5

Transient flora can be temporarily reduced, carried or changed, whereas resident is with your for life

Question 6

Why do babies faeces change?

Answer 6

As the baby acquires a microbial flora

Question 7

What are the stages in baby faecal transitions?

Answer 7

Sterile muconium -> facultative anaerobes -> bifidobacteria -> bacteriodes, clostridia and tobactera -> adult like gut microbiome

Question 8

What benefit are bifidobacteria to a baby’s gut?

Answer 8

Produce lactose, prevent the growth of gran negative bacteria and metabolise breast milk sugars

Question 9

What microorganisms can survive the stomach acid?

Answer 9

Lactobacilli and H. Pylori

Question 10

What microorganisms are found in the duodenum?

Answer 10

Lactobactilli and streptococcus

Question 11

What microorganisms are in the jejunum -> ileum?

Answer 11

Enterobacteria (Ecoli, klebsiella and bacterioles species)

Question 12

What microorganisms would you find in the colon?

Answer 12

Obligate anaerobes (Bacteriodes, clostridia and bifidobacteria) and facultative anaerobes (enterobacteria)

Question 13

What is the difference between obligate and facultative bacteria?

Answer 13

Obligate have to be anaerobic and facultative can be aerobic or anaerobic

Question 14

What are some other bacteria you could find in the colon?

Answer 14

Enterococci, staphylococci and lactobacilli

Question 15

How can you tell if someone has an illness by looking at their gut flora?

Answer 15

They have wildly different and varying bacteria

Question 16

What is dysbiosis?

Answer 16

Disruption of the normal flora (generalised diversity and species differences)

Question 17

What diseases correlate with dysbiosis (there are a lot!)?

Answer 17

• Inflammatory bowel disease
• ulcerative colitis
• crohns
• irritable bowel syndrome
• colon cancer
• allergies
• celiac
• both types of diabetes
• obesity
• mental health and depression

Question 18

What are the two ways of studying the microbiome?

Answer 18

Culturomics and genomics

Question 19

What are the two types of genomics?

Answer 19

16S rRNA gene profiling and shotgun metagenomics

Question 20

What are the aims of 16S rRNA gene profiling?

Answer 20

Identify taxonomic distribution of microbial species

Question 21

What is the basis of 16S rRNA gene profiling?

Answer 21

PCR based

Question 22

What are the aims of shotgun metagenomics?

Answer 22

Define the functional and sequence based diversity contained in all microbial genomes of communities

Question 23

What are the four types of host defences in the GIT?

Answer 23

Structural, mechanical, biochemical, immunological

Question 24

What are the structural defences in the GIT?

Answer 24

Seamless epithelium, tight junctions, sloughing/ turnover of epithelial cells

Question 25

What are the mechanical host defences in the GIT?

Answer 25

Peristalsis, chewing and fluid movement

Question 26

What are the biochemical host defences in the GIT?

Answer 26

Gastric acid, bile, mucus

Question 27

What are the immunological host defences in the GIT?

Answer 27

Secretory IgA and intra-epithelial lymphocytes

Question 28

What types of problems can you have to the host defences in the GIT?

Answer 28

Damage of barriers, pH change, overgrowth of organs and AIDS

Question 29

What are the four benefits of the gut flora?

Answer 29

- colonisation resistance - metabolites of benefit to host - Normal development of immunity - aids digestion

Question 30

What types of metabolites are of benefit to the host?

Answer 30

- Vit K2, B12 and organic acids - enhanced utilisation of amino acids - produces butyrate for colonocytes which maintain the anerobiasis

Question 31

How does the gut flora help the normal development of immunity?

Answer 31

Tolerance and antigenic stimulation (Tregs, IL17)

Question 32

How does the gut flora aid digestion?

Answer 32

- Fermentation of sugars (10% of energy) - H2 or methane gas - regulation of fat storage

Question 33

What are probiotics?

Answer 33

Organisms that can produce certain metabolites (lactic acid and other organic acids)

Question 34

What do probiotics do for us?

Answer 34

Allow us to absorb energy that we wouldn’t otherwise be able to

Question 35

How do probiotics allow us to absorb more energy?

Answer 35

Increasing the diversity of polysaccharides for metabolism

Question 36

What are prebiotics?

Answer 36

Nutrients that alter the gut ecosystem

Question 37

Give an example of a prebiotic

Answer 37

Bifidus factor in breast milk

Question 38

What are fermented in the colon by prebiotic organisms?

Answer 38

Certain oligosaccharides

Question 39

What do prebiotics do?

Answer 39

Promote growth of probiotes

Question 40

What are probiotics used for in medicine? (There’s a lot!)

Answer 40

``` Control diarrhoea in infants Relive constipation Improve digestion of lactose Restore normal gut flora Control candida growth Improve immune system Treat inflammatory bowel disorders reduce incidence of colon cancer Reduce cholesterol in blood Increase mineral absorption ```

Question 41

What is microbial antagonism?

Answer 41

When the normal flora limits the growth of competitors and pathogens

Question 42

What can happen if you loose a pathogen in the gut flora?

Answer 42

Bacterial or pathogenic overgrowth -> decreased diversity

Question 43

How long does it take for the gut flora to return to normal?

Answer 43

4 weeks

Question 44

What is a synonym for antibiotic associated colitis?

Answer 44

Pseudomembranous colitis

Question 45

What happens if there’s an overgrowth of clostridium difficile?

Answer 45

Cytotoxins, ulceration, severe diarrhoea, hospital cross infection risk

Question 46

What do you treat pseudomembranous colitis with?

Answer 46

Antibiotics

Question 47

What is your microbiome influenced by?

Answer 47

Diet, antibiotics, surgery and genes

Question 48

What does your microbiome contribute to?

Answer 48

Host metabolism and energy homeostasis

Question 49

What are the symptoms of gastroenteritis?

Answer 49

Nausea, vomiting, diarrhoea and abdominal discomfort

Question 50

What is dysentery?

Answer 50

Inflammatory GIT disorder- usually of the large intestine

Question 51

What is dysentery often associated with?

Answer 51

Blood and pus

Question 52

What are the symptoms of dysentery?

Answer 52

Pain, fever and abdominal cramps

Question 53

What is enterocolitis?

Answer 53

Inflammation involving the mucosa of the small and large intestine

Question 54

What microorganism is dysphagia caused by?

Answer 54

Candida

Question 55

What is dyspepsia caused by?

Answer 55

H. pylori

Question 56

What is infective proctitis caused by?

Answer 56

Ano-rectal STIs

Question 57

What is peritonitis?

Answer 57

Intra-abdominal abscess

Question 58

Give two examples of disease where there is local inflammation in response to superficial microbial invasion

Answer 58

Dysentery and food poisoning

Question 59

What is an enteric fever?

Answer 59

Deep invasion to blood and other lymphomas and dissemination of the organism to other body sites

Question 60

Give two examples of enteric fevers

Answer 60

Typhoid fever and Hep A

Question 61

What causes peritonitis?

Answer 61

Perforation/ulceration of mucosal epithelium

Question 62

How do exotoxins cause their effects?

Answer 62

Affect fluid/ electrolyte transport by increasing or decreasing cAMP

Question 63

How do cytotoxins cause their effect?

Answer 63

Stimulate second messengers to cause epithelial cells to secrete lots of water and chloride and stopping their reabsorption

Question 64

How do enteropathogens cause diarrhoea?

Answer 64

Sticks to the epithelial brush border forming an attaching and effacing lesion

Question 65

What are the four mechanisms of diarrhoea?

Answer 65

Bacterial toxins, adherence, penetration and invasion

Question 66

What toxins does entero-toxigenic E-coli produce?

Answer 66

LT, ST cGMP at membrane

Question 67

What are the virulence factors for E.coli?

Answer 67

Toxins, adhesions and invasins

Question 68

What does entero-toxigenic E.coli cause?

Answer 68

Travellers diarrhoea- secretory

Question 69

What mechanism does enteropathogenic E.coli use?

Answer 69

Attaching and effacing lesion

Question 70

What does entero-invasive E.coli cause?

Answer 70

Dysentery

Question 71

What mechanism of action does entero-haemorrhagic E.coli use?

Answer 71

Attaching/ effacing lesions

Question 72

What does entero-haemorrhagic E.coli cause?

Answer 72

Verotoxin, intense inflammation and HUS dysentery

Question 73

What are the steps in viral gastroenteritis?

Answer 73

Virus invasion -> cell death and villous atrophy -> crypt hyperplasia -> enteroblast replacement -> recovery