human microbiomes

Question 1

where are microbes found

Answer 1

microbes are found everywhere. we are continuously exposed to microbes. both exterior and internal cavities- anywhere that can get from the outside and the inside of our body.

Question 2

how many microbes are we exposed to everyday

Answer 2

billions

Question 3

what are the outcomes that can happen when we are exposed to microbes

Answer 3

-fail to colonise (majority of microbes)
- become short term residents (
- become long term residents

Question 4

define short term microbes

Answer 4

some cause disease (pathogens) but cleared by immune response. most are commensal that fail to establish because the house is ‘full’- unless they are able to displace or have specialised pathogens that can subvert normal hosts and occupy the sites.

Question 5

define long term residents

Answer 5

don’t cause disease. they contribute to many benefits to normal functions. first in fully occupy available sites for microbes.

Question 6

what are binary outcomes and define the types

Answer 6

based on winners and losers.
- parasitism: one winner and one loser
- commensalism: one winner no lose. need each other to live
- mutualism: two winners. permanent means mutualism but temporary means cooperation

Question 7

explain how to distiniguihost microbe interaction within he categories of binary outcomes

Answer 7

you need to assess outcomes overtime in both presence and absence for each interacting partner species.

Question 8

explain the limitations of using binary concepts to explain our relationship with microbes

Answer 8

life history can be very short in microbes for us to grasp the benefits. Another is that microbes are way way too small for us to understand

Question 9

what are the two outcomes we can use is we will base our interactions with microbes using binary concepts

Answer 9

1. accidental
2. commensal
   the only way for us to even know is if it has caused us harm.

Question 10

when do microbes begin to form in our bodies

Answer 10

after birth, the residence of trillions of microbes is normal.

Question 10

compare the weight of microbes and our mass

Answer 10

human 98% and microbe 2%. but there is actually more microbes than human cell because microbes are so much smaller.

Question 11

why is it important to understand how much microbes live in us.

Answer 11

natural selection. more microbes means that we are more able to adapt faster than our own body. by genes int eh gut, the microbial genome is several orders of magnitude higher than our human genome.

Question 12

what separate the place where microbes live and the rest of the body

Answer 12

the tight gut barrier is formed by mucin layer over tightly joint epithelial cells. it acts as a border.

Question 12

what is the koschs postulate

Answer 12

states that in the absence of the microbe the disease is no present. introduction of the organism is sufficient to cause disease

Question 13

define amensal

Answer 13

microbe never establishes a sustainable population in or on human body.

Question 14

what can parasite do to the body

Answer 14

they can establish long term population in human body that impairs performance

Question 15

what do pathogens do in the body

Answer 15

short term esbalsihment in/on human body that is associated with disease.

Question 16

do microbes always need to be infectious

Answer 16

no. major disease issue are chronic disease and are not infectious. they do however are associated with microbe differences.

Question 17

what explains the microbial differences that are seen to be associated with a disease.

Answer 17

it does not necessarily cause it but its difference in microbe is contributing to it. in health, we are in a coperitice community where they provide us with health benefits. but in a bad community state, there simply a breakdown in the operation of the body NOT introduction of the microbe but this is leading to lose in health benefits.

Question 18

what is the gut microbiome

Answer 18

it is sealed by a sphincter. the pyloric sphincter at the front separated the stomach from the small intestine, the ileocecal valve separates the small intestine from the colon and anal sphincter separates it from external world. duodenum - low moderate bacterial number - very high bacterial numbers

Question 19

do we just have one microbiome

Answer 19

no. the gut biome is the biggest however.

Question 20

what is the role of small intestine in the gut microbiome

Answer 20

small intestine is the biggest site of absorption and digestion. its rapid movement of material there keeps the microbe number quite low

Question 21

where do you find the microbiome in the gut

Answer 21

mostly in the clan and terminal ileum, very little in the stomach and tissues around the gut.

Question 22

what type of microbiome is mostly present in the gut

Answer 22

its made of 98% of bacteria. its mostly phyla- mostly bacteroidete and firmicutes and proteobacteria.

Question 23

ante natal experiments

Answer 23

a test to find what the microbiome is doing. this just means doing the experiment in the sterile environment. this essentially means you can raise them without microbes.

Question 24

what is the difference in organisms with microbiome present vs where there isnt

Answer 24

- the epithelial surface is different- the fucose that makes it yellow only becomes present torun day 14. this is also the same time that mice is colonised by bacteroid organisms that use fucose as their carbon source. - the gut vascularisation: vascularisation is greatly stimulated by the presence of microbes. it stimulates angiogenic pathways to ,are vessels. -IgA: in germ free animals, their adaptive immune system is not developed.

Question 25

what changes do we see in the absence of microbes

Answer 25

- gut functions: reduced digestive capacity - immune functions are different: essentially no adaptive immunity - metabolic regulation- altered neurological endocrine signalling pathways - cognitive functions and mood are different: undeveloped enteric nervous system.

Question 26

why is it important to have a steady microbiome

Answer 26

a stable gut microbiome is crucial in develops after birth and is key to post natal development.

Question 27

what is the stages that you acquire microbes and develop your microbiome

Answer 27

you develop your microbiome the same time you develop other critical post natal development stages. - gestation: no microbes. maternal microbes can contribute via the placenta to the foetus - infancy at birth, your microbiome begins to develop. the first 6 months when you're developing your microbiome, the starting point is very naive immune system and begins to develop complexity and cross talk with the microbiome as it also develops.

Question 28

why do you initially have a naive immune system

Answer 28

this is because of your very simple diet. breast milk, there is few nutrients coming in. post this, we begin to see a more complex network of microbes develop

Question 29

how does the development of the microbiome and immune system relate

Answer 29

they develop together.

Question 30

how do we get chronic diseases

Answer 30

they are hadn't in hand with changes in our food environment. these disturbances in early life cause deviations in microbiome homeostasis that interfere with the normal development of the immune system that then expose us to chronic disease especially allergies.

Question 31

how does the gut microbiome influence ability to absorb food

Answer 31

the presence of microbes changed our food requirements. we need to consider the action of microbes. in the presence of microbes, our energy harvesting ability is more sufficient ESPECIALLY in plant food. its also the quality- more vitamins are needed to keep germ free animals survive. this is because microbes supply daily mineral and vitamin requirements.

Question 32

where are most of the microbes and micro benefit come from

Answer 32

colon. material stays here longer to give them more time to perform their metabolic tricks.

Question 33

which macronutrients are best and least absorbed by out gut

Answer 33

fats and proteins are most essential because they can't always be taken anywhere else. we have trouble breaking down carbs with enzymes. enzymes are good at breaking down starch food, but not non starch food (plants with non starch polysaccharide)

Question 34

what happens to carbs that does not become glucose

Answer 34

it goes to the colon where the microbial carbohydrate degrading enzymes that break down the food convert them to soft chain fatty acids which we absorb from the colon

Question 35

what do calories mean in nutrition labels

Answer 35

energy you receive from food is released directly from it.

Question 36

what do energy from the short chain fatty acids mean

Answer 36

they are not molecules released from food. they are products of microbial action of the things that we release from food and then excreted from microbes. this means that different microbial activity can give rise to differences in the energy you can absorb. individual difference in microbe person top person means that there is difference in energy you can get.

Question 37

whats the difference in the contribution of microbes between animals, especially ruminants vs humans

Answer 37

the relative importance of that microbial contribution to animals vary according to function anatomy of their gut and their history. obligate herbivores (ruminants) have an extended chamber at the front of their gut, their microbe contribution can be up to 70% while we only have 10%

Question 38

how do what makes the fibre in our diet

Answer 38

polysaccharides

Question 38

how come polysaccharides can't get into bacteria

Answer 38

they are too big

Question 39

how does bacteria contribute to energy making.

Answer 39

they secrete enzymes to breakdown the polysaccharides and release monosaccharides from them. it doesn't use all the sugars it breaks down. you end up with a network of bacteria that shares the sugars.

Question 40

what are the types of sugars that can be released when the bacteria breaks down the food

Answer 40

polysaccharide but with glucose, many types of polysaccharides however have different types of sugars attached to them

Question 41

what is fermentative metabolism

Answer 41

bacteria using dissolved sugars as their source of energy. they do this to release energy. during their active growth, they produce waste products which is the shirt chain fatty acids hat contribute to energy harvesting for animals

Question 42

how do bacteria death benefit us

Answer 42

for bacteria to grow, it means that they are synthesising the proteins they need, the nucleic acid and the vitamins. when they die, we end up getting these nutrients= this is where the microbiome and nutrition fortify the environment of the gut.

Question 43

what are the main bacterial growths

Answer 43

- bacteroidetes - firmicutes both have fermentative metabolism and their preferred growth is polysaccharides. they are anaerobic - proteobacteria: capable of fermentative metabolism but use aerobic and anaerobic metabolism. this DOES NOT contribute short chain fatty acids

Question 44

why does the respiratory growth of the proteobacteria nt contribute to short chain fatty acids and why is it still beneficial

Answer 44

this is because it involves complete oxidation of glucose to carbondioxide and water. fermentation is a slow process that doesn't release a lot of energy.proteobacteria makes the environment in the colon anoxic. this means complete removal of oxygen which is needed by the other bacteria.

Question 44

what is the first colonisers of the infant gut

Answer 44

proteobacteria

Question 45

what does overgrowth of bacteria do.

Answer 45

overgrowth of bacteria - too much production of short chain fatty acids. along this is the production of carbondioxide and hydrogen . too high of this will lead to bloating. animals with their microbial activity at the front end of the gut will be harder for them to remove the gas.

Question 46

what causes leaky gut

Answer 46

overgrowth of sulfur reducing bacteria producing hydrogen sulfur.

Question 46

how does sulphate impact your body and where does it come from

Answer 46

anaerobic respiration from proceobacteria. sulfur as part of the amino acids is necessary for us to be healthy. the suffer reducing bacteria plays a role in this cycling. their waste products however is known as hydrogen sulphur which is toxic- means we can only have small amount of sulfur reducing bacteria.

Question 47

how do we control microbes

Answer 47

it is not the immune functions. the major way is by manipulating the phyla chimerical environment of the gut. they are managed to ensure they are continuously growing slowly at stable numbers and releasing short chain fatty acids

Question 48

what is the role of the immune system in terms of microbiomes

Answer 48

its to contain them. bacteria in the wrong place are eradicated. the immune system is carefully balanced to tolerate or remove them.

Question 49

how do pathogens get removed

Answer 49

1. colonisation resistance : when pathogens enter through the gut, they encounter the first line of defence. 2. barrier functions: mucin layer and tight junction to epithelial cells prevent live bacteria or their antigens getting through. 3. immune résponse: the immune tone is influenced by signals from the gut microbiome that impact maturation of regulatory T and B cells.

Question 50

what distinguishes commensal pathogen or specialised pathogen

Answer 50

specialist pathogen have weaponry that can directly cause disease like producing toxins that can damage normal function or through the immune system kicking in when there is

Question 51

immunopathology

Answer 51

it is the immune system kicking in causing symptoms as a response to the pathogen

Question 52

what happens after the immune system has removed the pathogen but fails to turn off

Answer 52

chronic low grade inflammation. this is known as dysbiosis.

Question 53

what is dysbiosis

Answer 53

its a term for diseases of a poorly functioning symbiosis. not cause by microbes. its inappropriate interaction between immune system and normal microbiome.

Question 54

what are the two types of immune response

Answer 54

DAMPs: pro inflammatory signals from cell damage (if micro is present or not) MAMPs pro inflammatory signals from microbes (including commensals)