intro to microbiology of the gut Flashcards
what is the human microbiome ?
- The collection of microbiota and their genomes in the human body
- Microbiota – Bacteria, archaea, fungi, protozoa, viruses that colonise our body surface
- mainly in the gut
- highly variable
describe the GIT
- Largest tube running through the body
- Comprises oral cavity, oesophagus, stomach, small intestine, large intestine
- Main function is digestion of food and absorption of nutrients
- Major surface for microbial colonisation (large surface area ~200m2, rich in nutrients)
describe the oral cavity
- Oral cavity – mouth, nose and throat
- Mouth is densely populated by microorganisms
Prevotella
Porphyromonas
Desulfovibrio
Bacteroides
Fusobacterium
Eubacterium
Peptostreptococcus
describe the stomach
- Stomach – J-shaped organ that receives food from the oesophagus
- Aids in chemical and mechanical digestion
- Low pH makes stomach almost sterile (<103 cfu/ml of gastric contents)
- Microorganisms in the stomach are transient rather than resident
- Acid-tolerant lactobacilli
- Yeasts
- Helicobacter pylori
what is helicobacter pylori ?
- Gram negative bacterium
- Colonises human stomach in early life
- 50% of the world’s population are carriers of H. pylori
- Disease occurs in about 15% - peptic ulcers, gastric inflammation (gastritis), gastric cancer
describe the small intestine
- Small intestine – digests and absorbs nutrients
- 3 parts – duodenum (upper part), jejunum and ileum (lower parts)
- Lower numbers (~103 per gram) due to secretion of bile and short transit time
- Higher bacterial number in ileum (up to 107 per gram)
Enterococci
Enterobacteria
Lactobacilli
Bacteroides
Clostridia
describe the large intestine
- Rapid increase in population in the large intestine (colon) (1012 per gram)
- Favourable for microbial growth due to favourable pH, nutrient availability and slow transit time
Bifidobacterium
Bacteroides
Eubacterium
Lactobacillus
describe the development of the gut microbiota
- The GI tract is sterile at birth
- Colonised by microorganisms from the mother and the environment
- Early colonisers are aerotolerant as gut initially contains oxygen; replaced by anaerobes
- Stabilises within the first few years of life
As many as 1000 species - Varying composition and numbers along the length of the GI tract
what are the factors that influence gut microbiota composition ?
Mode of delivery – vaginal vs caesarean section
Diet – breastfed vs formula fed
Antibiotic use
Age
Environment
what are the roles of microbiota in health ?
Digestion of food
Development of the gut immune system
Production of short-chain fatty acids
Production of essential vitamins
Resistance to colonisation by pathogens
describe the relationship between microbiota and disease
- Changes/alterations in microbiota (dysbiosis) are associated with various diseases
- Reduction in bifidobacteria and increase in other groups in commonly seen
- Altered community profiles of microbiota may be a cause or consequence of disease
describe different conditions and their bacterial observations
what is Bifidobacterium ?
- Anaerobic, non-motile heterofermentative Gram-positive rods
- Common inhabitants of the gastrointestinal tract
~90 species - Optimum growth conditions: 37-41˚C, pH 6.5-7.0
- Carbohydrate fermentation by fructose-6-phosphate phosphoketolase shunt
- Predominant in breast-fed infants
how do c sections , breast feeding and aging affect bacteria
what are probiotics ?
- Probiotics are live microorganisms which can confer a health benefit when administered in adequate amounts
- Dairy products are the most common vehicles for delivering probiotics
- Most common probiotic strains are members of Lactobacillus and Bifidobacterium
- Various health claims associated with probiotic strains
what are the health benefits associated with probiotics ?
- 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
how do these mechanisms work ?
what are the probiotic mechanisms of action ?
modulation of the intestinal ecosystem
improved colonisation resistance
modulation of immune resistance
what are prebiotics ?
- Substrates that are selectively utilised by host microorganisms, conferring a health benefit
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
describe breastmilk as a prebiotic
- Breast-fed infants have a microbiota dominated by Bifidobacteria compared to formula-fed infants.
- This is due to human breast milk containing bifidogenic factors, such as lactulose and human milk oligosaccharides (HMOs).
- These HMOs, including short-chain trisaccharides (e.g., sialyllactose) and complex glycans (e.g., N-acetyllactosamine polymers), are only partially digested in the small intestine.
- As a result, they reach the colon, where they selectively promote the growth of bifidobacteria in the gut microbiota.
what is a faecal microbiotica transplant ?
- FMT is the administration of a solution of faecal matter from a donor into the intestinal tract of a recipient in order to directly change the recipient’s microbial composition and confer a health benefit
what is gastroenteritis ?
An acute syndrome characterised by gastrointestinal
symptoms in any combination, including: nausea, vomiting, diarrhoea and abdominal discomfort
thought to be caused by an infection
what is diarrhoea ?
Defined as watery or liquid stools, usually with an
increase in stool weight above 200 g per day and an
increase in daily stool frequency and often a sense of urgency
Can lead to severe dehydration, excessive fluid and electrolyte loss; organ failure
Long-term morbidity and reduced growth
what is dysentery ?
Inflammatory disorder of GI tract – usually large intestine
Often associated with blood and pus in the faeces
Accompanied with pain, fever, abdominal cramps
what is enterocolitis ?
Inflammation involving mucosa of small and large intestine
what are some bacterial causes of diarrohea
Escherichia coli (Pathogenic E. coli – ETEC, EPEC, EIEC, EHEC)
coli
Salmonella
Campylobacter
Vibrio cholerae
Shigella
what are some viral causes of diarrhoeal disease ?
Noroviruses
Rotaviruses
Astroviruses
what is the damage that results from GIT infection ?
Pharmacological action of bacterial toxins local or distant to site of infection e.g. cholera
Local inflammation in response to superficial microbial invasion e.g. Shigella dysentery or Campylobacter food-poisoning
Deep invasion of blood and lymphatics and dissemination of organism to other body sites – enteric fevers e.g. Typhoid fever or Hepatitis A
Perforation/ulceration of mucosal epithelium after infection e.g. peritonitis, intra-abdominal abscess (e.g. Entamoeba)
what are the mechanisms of diarrhoea ?
Bacterial toxins: enterotoxins – affect the gut
Exotoxins – affect fluid/electrolyte transport by cAMP
Cytotoxins – direct cell damage
Adherence: damage to epithelium e.g. EPEC
Penetration and invasion
Disruption of tissue architecture and function
Inflammation
