Intro To Microbiology Of The Gut Flashcards
What is the microbiome?
Collection of bacteria, archea, fungi, Protozoa and viruses that colonise our body surface and their respective genomes and metabolic activities
What are the main bacterial phyla in the gut?
Firmicutes, bacteroidetes, actinobacteria and proteobacteria
What is the ratio of human cells: bacterial cells in the body?
1:1
What is a resident flora?
Your flora thats with you for life
What is the difference between transient and resident flora?
Transient flora can be temporarily reduced, carried or changed, whereas resident is with your for life
Why do babies faeces change?
As the baby acquires a microbial flora
What are the stages in baby faecal transitions?
Sterile muconium -> facultative anaerobes -> bifidobacteria -> bacteriodes, clostridia and tobactera -> adult like gut microbiome
What benefit are bifidobacteria to a baby’s gut?
Produce lactose, prevent the growth of gran negative bacteria and metabolise breast milk sugars
What microorganisms can survive the stomach acid?
Lactobacilli and H. Pylori
What microorganisms are found in the duodenum?
Lactobactilli and streptococcus
What microorganisms are in the jejunum -> ileum?
Enterobacteria (Ecoli, klebsiella and bacterioles species)
What microorganisms would you find in the colon?
Obligate anaerobes (Bacteriodes, clostridia and bifidobacteria) and facultative anaerobes (enterobacteria)
What is the difference between obligate and facultative bacteria?
Obligate have to be anaerobic and facultative can be aerobic or anaerobic
What are some other bacteria you could find in the colon?
Enterococci, staphylococci and lactobacilli
How can you tell if someone has an illness by looking at their gut flora?
They have wildly different and varying bacteria
What is dysbiosis?
Disruption of the normal flora (generalised diversity and species differences)
What diseases correlate with dysbiosis (there are a lot!)?
- Inflammatory bowel disease
- ulcerative colitis
- crohns
- irritable bowel syndrome
- colon cancer
- allergies
- celiac
- both types of diabetes
- obesity
- mental health and depression
What are the two ways of studying the microbiome?
Culturomics and genomics
What are the two types of genomics?
16S rRNA gene profiling and shotgun metagenomics
What are the aims of 16S rRNA gene profiling?
Identify taxonomic distribution of microbial species
What is the basis of 16S rRNA gene profiling?
PCR based
What are the aims of shotgun metagenomics?
Define the functional and sequence based diversity contained in all microbial genomes of communities
What are the four types of host defences in the GIT?
Structural, mechanical, biochemical, immunological
What are the structural defences in the GIT?
Seamless epithelium, tight junctions, sloughing/ turnover of epithelial cells
What are the mechanical host defences in the GIT?
Peristalsis, chewing and fluid movement
What are the biochemical host defences in the GIT?
Gastric acid, bile, mucus
What are the immunological host defences in the GIT?
Secretory IgA and intra-epithelial lymphocytes
What types of problems can you have to the host defences in the GIT?
Damage of barriers, pH change, overgrowth of organs and AIDS
What are the four benefits of the gut flora?
- colonisation resistance
- metabolites of benefit to host
- Normal development of immunity
- aids digestion
What types of metabolites are of benefit to the host?
- Vit K2, B12 and organic acids
- enhanced utilisation of amino acids
- produces butyrate for colonocytes which maintain the anerobiasis
How does the gut flora help the normal development of immunity?
Tolerance and antigenic stimulation (Tregs, IL17)
How does the gut flora aid digestion?
- Fermentation of sugars (10% of energy)
- H2 or methane gas
- regulation of fat storage
What are probiotics?
Organisms that can produce certain metabolites (lactic acid and other organic acids)
What do probiotics do for us?
Allow us to absorb energy that we wouldn’t otherwise be able to
How do probiotics allow us to absorb more energy?
Increasing the diversity of polysaccharides for metabolism
What are prebiotics?
Nutrients that alter the gut ecosystem
Give an example of a prebiotic
Bifidus factor in breast milk
What are fermented in the colon by prebiotic organisms?
Certain oligosaccharides
What do prebiotics do?
Promote growth of probiotes
What are probiotics used for in medicine? (There’s a lot!)
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
What is microbial antagonism?
When the normal flora limits the growth of competitors and pathogens
What can happen if you loose a pathogen in the gut flora?
Bacterial or pathogenic overgrowth -> decreased diversity
How long does it take for the gut flora to return to normal?
4 weeks
What is a synonym for antibiotic associated colitis?
Pseudomembranous colitis
What happens if there’s an overgrowth of clostridium difficile?
Cytotoxins, ulceration, severe diarrhoea, hospital cross infection risk
What do you treat pseudomembranous colitis with?
Antibiotics
What is your microbiome influenced by?
Diet, antibiotics, surgery and genes
What does your microbiome contribute to?
Host metabolism and energy homeostasis
What are the symptoms of gastroenteritis?
Nausea, vomiting, diarrhoea and abdominal discomfort
What is dysentery?
Inflammatory GIT disorder- usually of the large intestine
What is dysentery often associated with?
Blood and pus
What are the symptoms of dysentery?
Pain, fever and abdominal cramps
What is enterocolitis?
Inflammation involving the mucosa of the small and large intestine
What microorganism is dysphagia caused by?
Candida
What is dyspepsia caused by?
H. pylori
What is infective proctitis caused by?
Ano-rectal STIs
What is peritonitis?
Intra-abdominal abscess
Give two examples of disease where there is local inflammation in response to superficial microbial invasion
Dysentery and food poisoning
What is an enteric fever?
Deep invasion to blood and other lymphomas and dissemination of the organism to other body sites
Give two examples of enteric fevers
Typhoid fever and Hep A
What causes peritonitis?
Perforation/ulceration of mucosal epithelium
How do exotoxins cause their effects?
Affect fluid/ electrolyte transport by increasing or decreasing cAMP
How do cytotoxins cause their effect?
Stimulate second messengers to cause epithelial cells to secrete lots of water and chloride and stopping their reabsorption
How do enteropathogens cause diarrhoea?
Sticks to the epithelial brush border forming an attaching and effacing lesion
What are the four mechanisms of diarrhoea?
Bacterial toxins, adherence, penetration and invasion
What toxins does entero-toxigenic E-coli produce?
LT, ST cGMP at membrane
What are the virulence factors for E.coli?
Toxins, adhesions and invasins
What does entero-toxigenic E.coli cause?
Travellers diarrhoea- secretory
What mechanism does enteropathogenic E.coli use?
Attaching and effacing lesion
What does entero-invasive E.coli cause?
Dysentery
What mechanism of action does entero-haemorrhagic E.coli use?
Attaching/ effacing lesions
What does entero-haemorrhagic E.coli cause?
Verotoxin, intense inflammation and HUS dysentery
What are the steps in viral gastroenteritis?
Virus invasion -> cell death and villous atrophy -> crypt hyperplasia -> enteroblast replacement -> recovery
