Microbiome Flashcards
Animals harbour complex microbial community in intestines. What type of animal is it particularly important for? What two different kinds of this type of animal are there?
Herbivores (Foregut fermenters [ruminants: large fermentation chamber in stomach, regurgitates food for further chewing], Hindgut fermenters [fermentation takes place in large intestine, often eats poop to extract more nutrients])
Where do you find microbes in humans?
Which bacteria are most common in the gut?
Skin (1 million/cm3), oral cavity (1 billion/mL), stomach and duodenum (10-1000/mL), jejunum and ileum (0.01-100 million/mL), colon (10-100 billion/mL)
Firmicutes (60-70% of fecal bacteria), bacteroides (20-30% of fecal bacteria), actinobacteria, proteobacteria
Oral cavity, stomach/duodenum, small intestine, large intestine: pH and transit time differences?
Bacteria in the colon are _______ _________
Main sites of interaction with immune system?
Oral cavity (pH5-7, sec-min), stomach/duo (pH1-3, 1-2h), small inestine (pH 6-7.5, 1-5h), colon (pH5-7, 10h-days)
strictly anaerobic (less oxygen as you go through system)
Oral cavity, small intestine, and colon
At birth, gut is _______. First bacteria are from where?
What else tends to affect microbiota development?
How long does it take to develop adult microbiota?
What can affect microbiota overall? Which of these is most important?
Sterile. Vaginal/fecal natural, skin bacteria from caesarean
Breast feeding (bifidobacteria) or formula feeding (more complex)
Several years (and diet can make big varieties)
Genetic makeup, immune system, and environment (cleanliness, pets, diet, medications, etc) - environment seems to be most important
Early childhood is crucial for proper maturation of the immune system. What does it enable it to distinguish? Why is the microbiota important?
What is the hygiene hypothesis?
Resident microbiota and harmless environmental agents (tolerance), and pathogens (bacteria, viruses, fungi, parasites, etc - attack). We don’t know why exactly it is important, but we do know it is necessary.
Changes in microbiota due to lifestyle alterations + genetic predispositions = increases in allergies, asthma, autoimmune, etc.
What health conditions have been potentially linked to microbiota?
_____ overall microbial diversity is associated with several disease states
IBS, IBD, colorectal cancer, obesity, metabolic syndrome/diabetes, non-alcoholic fatty liver disease, depression, autism
Lower [NB: with all these things it could either be a causal relationship, or just a coincidence, so be aware when reading papers]
Beneficial and negative effects of microbiota? [4/4]
Benefit: barrier function against pathogens, immune maturation/stimulation, release and transformation of dietary molecules, production of metabolites (with positive end results)
Negative: opportunistic pathogens (that were commensal), may contribute to inflammatory diseases, release and transformation of toxic compounds from diet/environment, production of metabolites (with negative end results)
Microbiota-Diet-Host Interactions [picture summary]
What’s the main source of food for the microbiota?
What happens if we don’t get enough plant material and have too much proteins/fat?
Carbohydrates that we can’t digest (structural polysaccharides and non-digestible oligosaccharides) and remaining starch/sugars
Not much gets through to microbiome = toxins, carcinogens, and lower bacterial activity (lower supply of good metabolites, weaker barrier function)
Main substrates of dietary [4] and intestinal [1] origin for microbiota?
Resistant starch (fraction of dietary starch–amylose/amylopectin–that resists upper gut digestion and enters colon), non-starch polysaccharides (mainly plant cell wall components - cellulose, hemicellulose, pectins, gums, etc), resistant oligosaccharides (inulin, fructan from onions/artichoke/etc, etc), dietary protein
Mucus from the gut wall
What happens to the non-digestible carbs when they reach the microbiota? What three things are they mostly broken down to?
Acetate, butyrate, and propionate
Which bacteria converts starch to acetate?
Which bacteria converts acetate (or lactate) to butyrate?
Which converts lactate to propionate?
What converts oligo/monosaccharides to butyrate?
Bifidobacterium adolescentis
Eubacterium hallii
Coprococcus catus
Roseburia hominis
Short chain fatty acids (acetate, butyrate, and propionate) produced by gut bacteria give how much of our energy? Where is each one mainly metabolized?
What are the dual actions of butyrate (“butyrate paradox”)? WHat other effects does it have?
10% (Acetate = muscle and organs, propionate = liver, butyrate = colon)
Promotes proper function of healthy colon cells (main source of energy), but seems to inhibit growth of cancer cells [Others: anti-inflammatory, regulation of hunger/satiety]
What causes the pH differences in the proximal and distal colon?
Why might more diseases (eg: UC, colon cancer) start in distal colon?
[See pic]
Due to lower levels of bacterial activity (and fewer fermentation acids being formed)
What are phytochemicals?
What are xenobiotics?
How are the microbiota involved with these?
Different plant derived compounds also present in diet (includes many phenols - seem to be health promoting)
Anything not normally found in organism (drugs, pollutants, etc)
Organisms can release compounds (eg: fibre-bound phenolics) or biotransform them into other compounds - they can then operate differently with host machinery, and effect physiology
What is the exchange between metabolism of microbiota and host called? Give an example
Enterohepatic circulation (dietary polyphenols with sugar attached - bacterial glycosidase cleaves off sugar, turning it into an aglycone - this is taken up by the liver, and has B-glucaronic acid attached, and returned to the gut - bacteria then slices off acid (to also use as food stuff, etc)
What does DGGE stand for? What is it used for? How does it work?
Denaturing Gradient Gel Electrophoresis (profiling microbe community). You take your sample and do PCR amplification of the 16S rRNA gene - one of the primers has a 40-GC-repeat (more hydrogen bonds) clamp. You then put them through gel electrophoresis with a concentration gradient of a denaturing agent - as the 16S genes will have differences, they will (mostly) break apart at different times (held together by clamp), and this differential break-up will affect their movement speed through the gel. In this way, you can identify differences in microbe composition, and potentially choose what to sequence.
DGGE is one of the techniques for looking at the broader microbe community. What does this stand for, and what was the other one mentioned? How does it work?
Denaturing Gradient Gel Electrophoresis. The other one was Terminal Restriction Fragment Length Polymorphism (tRFLP). You do PCR on the 16S rRNA gene, but one of the primers contains a clamp with a fluorescent dye. Once this has occurred, you put in restriction enzymes that cut the bacteria at certain (different depending on variable regions) points, creating strands with different lengths. These are then separated by length through capillary electrophoresis (and detection of the fluorescence).
Highlight the experimental approaches (in regards to the microbiome) that you might take with human volunteers…
Prebiotic inulin study: which bacteria went up in numbers significantly? What do they do?
NB: big inter-individual differences (would really need more people)
Fully controlled dietary trial (look at carb intake differences): what healthy metabolite was massively reduced? What was increased?
NB: Grey = maintenance carbs, pink = mod carb, purple = low carb
Takehome: high protein diets are dangerous, and get moreso if you don’t get enough carbs
