Introduction to the Microbiome of the Gut Flashcards
How many species does the normal flora include?
> 1000s of species of bacteria (more than 15,000)
Define microbiome and microbiota
Microbiome - the collection of bacteria, archaea, fungi, protozoa and viruses (the microbiota) that colonise our body surface and their respective genomes and metabolic activity
What is the microbiome highly variable between?
People, sites, disease states etc
What does microbiome play a major role in?
Play a major role in human health and disease
What phyla dominate the flora?
Firmicutes, bacteroidetes, actinobacteria and proteobacteria
Describe what our genetic landscape and metabolic feature are encompassing flora
Our genetic landscape -
- A summation of the genes embedded in our genome
- And the collective genomes of our habitat associated microbial communities
Our metabolic features -
- An amalgamation of human and microbial attributes
Describe where flora are present and what resident and transient flora are
- All surfaces of the gut are covered with flora
- Resident flora are present for life while transient flora are temporarily reduced, carried or changed
Describe how flora changes in babies
- From a baby to an adult there are changes - weaning of a breast milk diet means bifidobacterium which is over 90% but as the baby grows the diet, environment, stess, hormones, age and transit time change so the microbiome changes
- The baby first produces sterile meconium
- As the baby acquires microbial flora they have facultative anaerobes and then a strictly anaerobic gut during which stool is green
- The breast fed baby eventually has yellow stool as the bifidobacteria (gram + bacteria that produce lactic acid and prevent gram - bacteria growth) from breast milk changes the flora to more adult like microbes of bacteroides, clostridia and eubacteria (gram - bacteria)
What relationships are included in symbiosis
Commensalism, mutualism
Describe how the distribution of flora changes throughout the gut
- The number of flora present increases as you move from the oesophagus towards the anus
- In the oesophagus and fundus of the stomach it is sterile as few flora are ound here
- In the stomach there is a few lactobacilli and infections like H pylori can reside here
- Then in the duodenum there is lactobacilli and streptococcus
- In the jejunum/ileum there is enterobacteria like e coli, klebsiella bacteriodes spp
- In the large intestine there is both obligate anaerobes (bacteriodes, clostridia, bifidobacteria) and facultative anaerobes (enterobacteria - E.coli, klebsiella, proteus)
- Then in the rectum/anus there is enterococci, staphylococci, lactobacilli - highly variable between people
State what dysbiosis is and state some conditions associated with it
- Dysbiosis - (lack of equilibrium shown by normal gut flora)
- Inflammatory bowel disease - ulcerative colitis and crohn’s disease
- Irritable bowel syndrome
- Clostridium difficile
- Colon cancer
- Allergies
- Coeliac disease
- Diabetes type I and II
- Obesity
- Mental health and depression
How is the microbiome studied?
- Culturomics
- Genomics - 16s rRNA gene profiling - aims to identify taxonomic distribution of microbial species
- Shotgun metagenomics - sequence all DNA in sample to define the functional and sequence based diversity contained in all microbial genomes in communities
What are our defences for abnormal flora?
- Structural - seamless epithelium, tight junctions, sloughing/turnover
- Mechanical - peristalsis, chewing, fluid movement
- Biochemical - gastric acid, bile, mucous
- Immunological - secretory IgA, intraepithelial lymphocytes
State the benefits of gut flora
- Colonisation resistance - blocks pathogens
- Metabolites of benefit to host - vitamin K2, vitamin B12, organic acids, enhanced utilisation of amino acids
- Normal development of immunity - tolerance, antigenic stimulation
- Aids digestion - fermentation of sugars, regulation of fat storage
Describe probiotics and prebiotics
- Probiotics -
- Best probiotic organisms produce lactic and organic acids
- They increase the diversity of polysaccharides for metabolism e.g. raffinose and stachyose in beans are unabsorbable without flora
- E.g. lactobacillus acidophilus, bifidobacteria, some streptococci
- Prebiotics -
- Prebiotic nutrients alter the gut ecosystem
- Certain oligosaccharides fermented in the colon by probiotic organisms promote the growth of probiotics
What are probiotics used for in medicine?
- Control diarrhoea in infants
- Relieve constipation
- Improve digestion of lactose
- Restore normal gut flora after antibiotics
- Control yeast growth
- Improve immune system
- Treat inflammatory bowel disorders
- Reduce colon cancer incidence
- Reduce cholesterol in blood
- Increase mineral absorption
What does microbial antagonism do?
- Maintains the flora
- Limits the growth of competitors and pathogens
What can flora do to control flora numbers?
- Produce Bacteriocins
- Reduced numbers of available epithelial receptors
- Keep pH low
- Controls oxidative potential
- Limits pathogen growth
- Occupies all niches
- High numbers
- Waste products prevent pathogen growth
What does a loss of flora lead to and what causes it?
- Leads to bacterial or pathogen overgrowth
- Ciprofloxin decreases diversity with significant effects on 1/3rd of taxa
- E.g. antibiotic associated colitis - clostridium difficile in low numbers in the gut but it can overgrow and produce cytotoxins which leads to ulcerations due to inflammation, severe diarrhoea etc which is treated with antibiotics
Describe stimuli that impact the microbiome and how the GI reacts to these
- Stimulus -
- Caloric uptake
- Nutrient composition
- Antibiotics
- Genetic influence
- Bacterial exposure
- GI surgery
- Response -
- Neuroendocrine appetite regulation
- GI peptide hormones
- Gut glucose production
- GI nutrient digestion/absorption
- Gut lipid production
- Inflammatory signals
Define diarrhoea
Diarrhoea is defined as watery or liquid stools usually with an increase in stool weight above 200g per day and an increase in daily stool frequency and a sense of urgency
State the clinical consequences of diarrhoea
- Can lead to severe dehydration excessive fluid and electrolyte loss - hypovolaemia, hypokalaemia and organ failure
- There is long term morbidity and reduced growth
Define 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
Define dysentery
Inflammatory disorder of the GI tract - usually the large intestine - often associated with blood and pus - pain, fever, abdominal cramps
Define enterocolitis including what C jejuni enteritis affects
Enterocolitis - inflammation involves mucosa of small and large intestine
C. jejuni enteritis - infects the jejunum, ileum and then colon
Describe the impact of diarrhoeal diseases on the world
- 3 billion episodes a year
- 550,000 deaths a year usually due to dehydration
- Massive global health burden that is preventable
- Can be due to infections - microorganisms like bacteria, viruses and parasites - this can be transmitted to new hosts
Describe some patterns of gut infections
- Acute watery diarrhoea
- Acute or chronic diarrhoea + blood and pus is dysentery
- Chronic diarrhoea as well as malabsorption - poor fat absorption
- Infective proctitis - ano-rectal STIs
- Enteric fevers e.g. typhoid - systemic infections
- Dyspepsia - ulcers H.pylori
- Dysphagia - oesophagus and candida
Describe the 4 types of damage that can result from GI tract infections
- 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 to blood and lymphatics and dissemination of the organism to other body sites - enteric fevers e.g. typhoid fever or hepatitis A
- Perforation/ulceration of mucosal epithelium - peritonitis - intra abdominal abscess e.g. entamoeba
State the 2 types of bacterial toxins that impact the gut
Exotoxins affect fluid/electrolyte transport by changing cAMP
Cytotoxins - direct cell damage
Describe how heat stable toxins of Ecoli affect the gut
- Toxin binds to a receptor on the surface on an enterocyte
- This stimulated guanylate cyclase to convert GTP to cGMP
- This activated protein kinases which cause phosphorylation of Cl- channels which changes the electrolyte balance and causes water loss which causes diarrhoea
Describe how heat labile toxins of Ecoli affect the gut
- This toxin has multimeric protein with 2 binding units and 2 activity units
- The binding site bind to receptors on the enterocyte surface
- The activity unit penetrates the enterocyte and stimulates G alpha S subunit
- This stimulates adenylate cyclase to cause to formation of cAMP from ATP
- This stimulates protein kinases which phosphorylate Cl- channels and change electrolyte balance and causes water loss which causes diarrhoea
How does enteropathogenic Ecoli damage the epithelium via adherence
- The e coli destroys the brush border and tightly attaches to the cell underneath
- This forms a lesion on the surface
- There is also microvillus elongation
- Hence damage occurs 2 fold from the E.coli toxins and its damage to the brush border of the gut
What happen when microroganisms penetrate and invade the epithelium
- Disruption of tissue architecture and function
- Inflammation
Why is Ecoli both good and bad in the body?
Because it can act as a commensal but some strains have gained virulence factors that make them have negative effects (become pathogenic)
State and describe the different types of Ecoli and how they damage the gut
- ETEC (enterotoxigenic E Coli) -
- Causes travellers diarrhoea
- No inflammation or structural changes to brush border
- Releases toxins like cholera toxins at the membrane surface
- EPEC (enteropathogenic E Coli) -
- Binds to epithelial cells to damage the brush border
- Also secretes toxins
- EIEC (enteroinvasive E Coli) -
- Very invasive and inflammatory
- Destroy the brush border and spread throughout the epithelium once it is infiltrated
- EHEC (enterohemorrhagic E Coli) -
- Intense inflammation
- Destroys the brush border and secretes strong toxins that enter the blood circulation and damage the kidneys - causes urinary tract/kidney infections or septicaemia
How do viruses damage the GI mucosa?
- Viral infection of epithelium
- Cell death and villous atrophy
- Crypt hyperplasia
- Enteroblasts must be replaced and eventually recovery occurs
