Introduction to the microbiology of the gut

Question 1

Explain characteristics of the human microbiome

Answer 1

Microbiome- the collection of microbiota and their genomes in the human body
-70% of total microbes found in the gut
-100 trillion microbial cells
Microbiome plays important roles in human health and disease

Question 2

Describe the human microbiome in different areas of the body

Answer 2

As you descend down the GI tract:
-number of microbiome increases
-stomach has the lowest amount of microbiome

Question 3

Explain the human GI tract

Answer 3

-largest tube running through body
-comprises oral cavity, oesophagus, stomach, small intestine and large intestine
-main function is digestion of food and absorption of nutrients

Question 4

Explain the oral cavity and microorganisms in it

Answer 4

-oral cavity: mouth, nose and throat

Microorganisms in the oral cavity:
-prevotella
-porphyromonas
-desulfovibrio
-bacteroides
-fusobacterium
-eubacterium
-petostreptococcus

Question 5

Explain characteristics of the stomach

Answer 5

stomach- J shaped organ that receives food from the oesophagus
-aids in chemical and mechanical digestion
-low pH makes stomach almost sterile
-microorganisms in the stomach are transient rather than resident

Examples of microorganisms in stomach:
-acid tolerant lactobacilli
-yeasts
-helicobacter pylori

Question 6

Explain characteristics of the helicobacter pylori

Answer 6

-gram negative bacterium
-colonises human stomach
-50% of the worlds population are carriers of H.pylori
-disease occurs in about 15% (peptic ulcers etc)

Question 7

Explain characteristics of the small intestine and microorganisms in it

Answer 7

-small intestine (digests and absorbs nutrients)
-3 parts (duodenum, jejunum, and ileum
-lower numbers of microorganisms due to secretion of bile
-higher bacterial number in ileum

Examples:
-enterococci
-enterobacteria
-lactobacilli
-bacteroides
-clostridia

Question 8

Explain characteristics of large intestine and examples of microorganisms

Answer 8

-rapid increase in population in large intestine
-favourable for microbial growth due to favourable pH

Examples:
-bifidobacterium
-bacteriodes
-eubacterium
-lactobacillus

Question 9

Explain the development of the gut microbiota

Answer 9

-the GI tract is sterile at birth
-colonised by microorganisms from the mother and environment
-early colonisers are aerotolerant as gut initially contains oxygen
-as many as 1000 species

Question 10

What are factors influencing gut microbiota composition

Answer 10

1) mode of delivery
-diet
-antibiotic use
-age
-environment

Question 11

what are the roles of intestinal microbiota in health

Answer 11

-digestion of food
-development of the gut immune system
-production of short chain fatty acids
-production of essential vitamins
-resistance to colonisation of pathogens

Question 12

What is the relationship between microbiota composition and disease

Answer 12

1) changes in microbiota are associated with various diseases

2) reduction in bifidobacteria and increase in other groups are commonly seen

3) altered community profiles of microbiota may be a cause or consequence of disease

Question 13

Explain the observations of antibiotic associated diarrhoea and chronic C.difficile infections

Answer 13

-reduced diversity
-increase in enterobbacteriacea and firmicutes
-reduced levels of bifidobacterium
-sp. And baceriodetes

Question 14

Explain observations of irritable bowel syndrome and inflammatory bowel disease

Answer 14

irritable bowel syndrome:
-increase in firmicutes
-reduced levels of bacteroidetes and bifidobacterium

Inflammatory bowel disease:
-reduced diversity
-lower levels of faecalibacterim
-increase in enterobacteriaceae
-reduced levels of bifidobacterium sp. In pediatric IBD

Question 15

Explain observations of atopic disease

Answer 15

-increase in clostridium sp.
-reduced levels of bifidobacterium sp.

Question 16

Explain characteristics of bifidobacterium

Answer 16

-anaerobic, non motile heterofermentative gram positive rods
-common inhabitants of GI tract
-90 species
-optimum growth conditions 37-40 degrees celcius and alkaline pH

Question 17

What are observations of bacteria in a Caesarean section, infant feeding and ageing

Answer 17

Caeserean section:
-higher numbers of the Clostridium difficile group 1
-delayed colonisation with bifidobacterium sp., Lactobacillus sp. And bacteroides sp.

Infant feeding:
-formula fed infants with lower levels and diversity in Bifidobacterium sp.

Ageing:
-increase in enterobacteriaceae and bacteroidetes
-reduced levels of bifidobacterium sp.

Question 18

Explain the population of bifidobacteria throughout life

Answer 18

-population of bifidobacteria decreases with age
-highest at infancy, declines and remains stable at adulthood
-further decline at elderly age—-> linked with increased susceptibility to GI disorders in the elderly

Question 19

Explain modulation of gut microbiota composition

Answer 19

-dietary interventions
-faecal microbiota and transplantation

Question 20

Explain probiotics

Answer 20

-probiotics are live microorganisms which can confer a health benefit
-diary products are the most common vehicles for delivering probiotics
-most common probiotic stains are members of lactobacillus and bifidobacterium

Question 21

What are the health benefits associated with probiotics

Answer 21

-prevention of diarrhoea
-alleviation of lactose intolerance
-control of IBD/IBS
-cancer prevention
-cholesterol reduction
-modulation of the immune system
-establishment of healthy microbiota in premature infants

Question 22

What is probiotic mechanisms of action?

Answer 22

Probiotic benefits may occur directly or indirectly directly by a number of mechanisms:
-modulation of the intestinal ecosystem
-improved colonisation resistance
-modulation of immune resistance

Question 23

Explain what happens in the mechanism of modulation of intestinal ecosystem

Answer 23

-the consumption of probiotics and transient colonisation that occurs can influence the composition and activity of the natural gut microbiota and help maintain a beneficial balance

-occurs by increasing population of beneficial bacteria + decreasing pop of harmful microorganisms

-achieved by production of organic acids or short chain fatty acids (lower gut pH)

-gut made more favourable to beneficial bacteria (e.g. lactobacilli and bifidobacteria)

Question 24

Explain improved colonisation resistance

Answer 24

-the growth and metabolism of probiotic microorganisms can alter the intestinal environment such that colonisation resistance is improved.

-may result from adhesion to epithelial cells by probiotics (thus blocking the adhesion of pathogens) as well as the stimulation of mucin production which enhances which enhances intestinal barrier function.

Question 25

Explain the modulation of immune resistance

Answer 25

-probiotics can stimulate mucosal immunity + modulate immune responses by their interaction with GALT -GALT is the largest lymphoid tissue in the human body -metabolites, cell wall components, and DNA of probiotic microorganisms are recognised by host cells that are sensitive of them -activation of these receptors leads to modulation of pro- and anti-inflammatory cytokine expression

Question 26

Explain the probiotic mechanism of the modulation of immune resistance

Answer 26

-stimulation of local and systemic systems -enhanced defence response (increased IgA, CD4 + CD8 + T cells, NK cell activity) -downregulation of inflammatory and allergic response

Question 27

Explain the probiotic mechanism of activity for improved colonisation resistance

Answer 27

-increased competitive exclusion -reduced harmful microbial species -increased epithelial cells mucin synthesis -enhanced intestinal barrier function

Question 28

How do probiotics help protect our gut from pathogens?

Answer 28

1) Pathogen Exclusion Probiotics physically block harmful pathogens from attaching to our intestinal 3cells. 2) Immune Stimulation Probiotics can stimulate the immune system by interacting with immune cells, helping your body to defend itself better. 3) Competition for Nutrients Probiotics compete with pathogens for food — leaving less for the harmful bacteria to grow. 4) Antimicrobial Substances and Direct Antagonism Probiotics produce substances that can directly kill or inhibit the growth of pathogens. 5) Barrier Function Probiotics strengthen the intestinal wall, making it harder for pathogens to get inside your body. 6) Reduction of Inflammation Probiotics can help calm down inflammation in the gut by promoting anti-inflammatory molecules like IL-10 and reducing pro-inflammatory ones (like TNF-α, IL-6, etc.).

Question 29

Explain health claims regulation

Answer 29

-very few health claims related to probiotics have been approved by authorities -this is due to unsatisfactory dossiers -many manufacturers now favour the use of descriptors such as ‘beneficial bacteria’ -‘probiotic’ implies health benefit and is therefore subject to scrutiny

Question 30

Explain how prebiotics occur

Answer 30

substrates that are selectively utilised by host microorganisms, conferring a health benefit

Question 31

Explain the prebiotic criteria

Answer 31

Prebiotic criteria: -resistant to gastric acidity —-> hydrolysis by enzymes and gastrointestinal absorption -fermented by intestinal microbiota -selectively stimulate growth and/or activity of intestinal bacteria associated with health and wellbeing

Question 32

What are 5 examples of prebiotic compounds

Answer 32

-Inulin -FOS -GOS -XOS -IMO

Question 33

What are natural sources of prebiotics

Answer 33

-agave -banana -garlic -onions -leeks

Question 34

Describe the two different types of substances that affect our microbiome

Answer 34

Prebiotic — substances that our gut microbes can selectively use to grow and stay healthy. Not Prebiotic — substances that affect the microbiome, but are not considered prebiotics. Prebiotics (the good food for microbes): These are selectively used by beneficial gut bacteria and include: CLAs and PUFAs (types of healthy fats) Human milk oligosaccharides (special sugars found in breast milk) Oligosaccharides like: FOS, Inulin, GOS, MOS, XOS (types of plant fibers) Phenolics and Phytochemicals (plant compounds with health benefits) Prebiotics can also be part of dietary fiber: Readily fermentable (quickly digested by microbes) Less fermentable (digested more slowly) Not Prebiotic (but still important) These influence the gut microbiome but are not classified as prebiotics: Proteins and fats Probiotics (live beneficial microbes) Antibiotics (can harm or wipe out microbes) Vitamins (important for health but not food for microbes)

Question 35

Explain breast milk as a prebiotic

Answer 35

-Bifidobacteria predominate the microbiota found in breast fed infants -human breast milk has been found to be contained to bifidobacteria -oligosaccharides are only partially digested in the small intestine and are therefore unable to reach the colon to selectively stimulate the development of bifidobacteria in the gut microbiota

Question 36

What is faecal microbiota transplantation (FMT)

Answer 36

FMT is the administration of a solution of faecal matter from the donor into the intestinal tract of a recipient in order to directly change the recipient’s microbial composition and confer a health benefit

Question 37

Explain what can happen due to a C difficult infection

Answer 37

-irritable bowel syndrome -inflammatory bowel disease -ulcerative colitis -Crohn’s disease

Question 38

What are terms used to describe GI tract infections

Answer 38

-gastroenteritis -diarrhoea -dysentery -enterocolitis

Question 39

Explain characteristics of gastroenteritis

Answer 39

-an acute syndrome characterised by gastrointestinal symptoms in any combination: -nausea, vomiting, diarrhoea and abdominal comfort -thought to be caused by infection

Question 40

Explain characteristics of diarrhoea

Answer 40

-defined as watery or liquid stools (increase in stool weight above 200g per day) -can lead to severe dehydration -long term morbidity and reduced growth

Question 41

Explain characteristics of dysentery

Answer 41

-inflammatory disorder of GI tract- enlarged large intestine -often associated with blood and pus in the faeces -pain, fever and abdominal cramps

Question 42

Explain characteristics of entercolitis

Answer 42

-inflammation involving mucosa of small and large intestine

Question 43

What is the impact of diarrhoeal diseases

Answer 43

-3 billion episodes per year -preventable -infectious microorganisms -shed in faeces -faecal-oral route

Question 44

What are bacteria species that cause diarrhoeal diseases

Answer 44

-E.coli -ETEC, EPEC, EIEC, EHEC -Salmonella -Compylobacter

Question 45

What are the different viral species involved in diarrhoeal disease

Answer 45

-noroviruses -rotaviruses -astroviruses -SRSVs

Question 46

What are different damages that result from infection of GI tract

Answer 46

-pharmacological action of bacterial toxins local or distant -local inflammation in response to superficial microbial invasion -deep invasion of blood and lymphatics

Question 47

Explain two different bacterial toxins that can result in diarrhoea

Answer 47

bacterial toxins: enterotoxins- affect the gut Exotoxins- affect fluid/electrolye transport by cAMP Cytotoxins-direct cell damage

Question 48

What is adherence in mechanisms of diarrhoea

Answer 48

damage to epithelium (EPEC)

Question 49

Explain penetration and invasion as a mechanism of diarrhoea

Answer 49

-disruption of tissue architecture and function -inflammation