Exam 4

Micro

Symbiosis

the relationship between microbes or living organisms.

Ectosymbiont

Organism is located on the surface of the cell

What are some examples of an ectosymbiont

Fleas and ticks because they do not enter the host, they are attached to the surface, suck the life out of something and then fall off and die.

Endosymbiont

Organism which is located inside another

what is an example of an endosymbiont

viruses or bacteria

Consortium

a host with more than one associated symbiont

What is an example of an consortium and why

Humans are consortiums

* we have interactions between our cells and microbes, both positive and negative interactions.
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What are the two types of consortiums?

intermittent/cyclic - they are either temporary (they come and leave and stay gone) or they are cyclic (the come and then leave and then come back)

permanent interactions (these come and they never leave)

What are some permanent interactions in our body.

E. Coli is found in our gut, and this something that is forever-

What is an example of a intermittent/cyclic interaction

Candida albicans

What are the three positive microbial interactions?

Mutualism

cooperation

commensalism

What are the 4 negative microbial interactions

Predation (killing)

Parasitism (exploitation)

Ammensalism

competition

What is mutualism?

This is when A helps B and B helps A.

* there is a dependence on each other, so if you were to take A away then B would die.
* i help you and you help me.

What are two examples of a mutualistic interactions?

* Aphids (insect) and B. aphidicola (bacteria)
* Termites and Trichonympha (protist) and Elusimicrobium Bacteria

How does the relationship between Aphids and B. aphidicola work?

* They have coevolved.
* The bacteria grows in the gut of the insect. the insect already has bacteria growing in the gut as an embryo.
* The bacteria is almost like an organ to the insect the insect now depends on the B. aphidicola to make whatever it is making for the aphid.
* the bacteria benefits because it get nutrients and shelter from the insect.

How does the protozoan-termite-bacteria relationship work?

* the Trichonympha breaks down the wood (lignocellulose) for the termite while also taking some of the glucose from it. The termite can no longer breakdown the wood itself.
* The termite provides food for the protozoan (tichonympha)
* inside the protist there is also a bacteria (elusimicrobium), and the protist (trichonympha) relies on the bacteria like the termite relies on the protist.
* The bacteria is found to do nitrogen fixation so that way the protist can take nitrogen and incorporate it into their 12 carbon skeletons to make amino acids and everything else.

Cooperation

A helps B and B helps A, however you can separate B and A

it is a positive symbiosis that benefits both organisms. They can grow apart but they grow much better together

What are some examples of cooperation?

* The relationship between a bacteria and a nematode
* the relationship between bacteria and humans

How does the cooperative relationship between a bacteria and nematode work?

Inside the nematode is the actual bacteria.

* That bacteria grows in the gut of the nematode
* the nematode is going to find some kind of cocoon and insert itself inside of the cocoon as the butterfly is going through the process of changing.
* when the nematode enters it will actually release the bacteria from its gut and now both the bacteria and the nematode are going to start killing the butterfly, and as they kill the butterfly they start absorbing its nutrients. So both the nematode and the bacteria are gaining from this.
* they can keep doing this together but they can also separate and do it on their own.

How does the cooperative relationship between bacteria and humans work?

* we see that there is a nice positive relationship between humans and bacteria
* we give them nutrients and protection
* bacteria give us nutrients, compounds that can help with decreased inflammation in the gut, and somewhat protection from pathogens.

What is commensalism?

it is a positive microbial interaction.

* one organism benefits (commensal) and the other is neither harmed nor helped. it is a unidirectional relationship.

The commensalism interaction is often _____?

syntrophic (cross feeding)

* this is a modification of the environment.

What are some examples of commensalism?

Nitrification

Microbial succession during spoilage of milk.

Formation of biofilms

Sharks and fish.

How does the commensalism relationship of nitrification work?

Nitrification is (NH3→ NO2→ NO3)

* formation of nitrosomonas is the first step; formation of nitrobacter is the second step.
* Nitrobacter depends on Nitrosomonas because nitrosomonas will take the substrate and make it into a waste product, and then the nitrobacter will take the wast which is subtrate and make its own was product.

How does the commensalism relationship of microbial succession during spoilage of milk work?

* Milk is not sterile-milk is pasteurized which means there is a decrease in microbes
* As the microbes in our milk increase, they will start breaking down the protein in the milk
* bacteria can even change the pH of milk.
* As there is a change in our milk, there are different bacteria that are going to take over or start to grow better.
* as the environment changes, it becomes better for somebody else and they may end up taking over.

How does the commensalism relationship in biofilms work?

* Biofilms form on hard surfaces, but one thing that has to be laid out on that hard surface are these proteins or polypeptides that help with adherence.


* not only are bacteria laying that out but they are the ones who create the landing pad. once the landing pad is laid out, other bacterias combine and we can create that biofilm.

How does the commensalism relationship of sharks and fish work?

* The fish are gaining protection by swimming close to the shark. and the shark is not gettin anything in return.

Describe the predation microbial interaction

* the smaller predator goes after the prey and the prey will always be killed. The predators will obtain chemical precursors and energy after the prey is dead.

What are some example of bacterial predation?

Bdellovibrio

Vampirococcus

Daptobacter

Myxococcus

How does the predator Bdellovibrio work?

* it penetrates the cell wall and grows outside of the plasma membrane so they are technically not going inside of the cell just in the periplasmic space.
* Bdellovibria will grow and replicate once they are inside of the periplasmic space. This will kill the cell from the outside in.
* The bacteria will lyse the cell, absorb all of the nutrients and move on.

How does the predator Vampirococcus work?

* As vampires, they use an apibiotic mode of attacking its prey.


* they are ectosymbionts, meaning they stay outside and do not enter the cytoplasm.
* Vampirococcus’s attach and suck the life out of their prey, just like a vampire does.

How does the predator Daptobacter work?

* Daptobacter penetrate the prey and then directly consumes the cytoplasmic contents
* this bacteria will go ahead and enter the cytoplasm it will cross the cell wall and the cell membrane into the cytoplasm, and then it kills it from the inside out.

How does the predator myxococcus work?

* these “wolf pack” cells use gliding motility to creep overtake their prey and release degradative enzymes.
* Once Myxococcus get to a high number, the colony becomes too large and bacteria have to get away from it.
* They start moving to get new space and look for food.
* They release some kind of chemical that does the killing, and as they kill them myxoccocus absorbs the nutrients.
* the chemical compound they release depends on the environment and the species of myxococcus.
* \

Which one of the example predators is a facultative predator?

Myxococcus

Describe parasitism.

* this is a negative interaction for the host because the parasite is going to take something from them.
* the parasite will not kill the host, if they kill the host they will have to search for a new one.
* one organism gains (parasite ) while the other is harmed (host)
* Parasites will obtain biochemical precursors and energy while the prey is still alive.
* Successful parasites have evolved to coexist in equilibrium.

What Microbial interactions experience genomic reduction?

Successful parasites that live in equilibrium with their host

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Mutualism

Describe amensalism

* the negative impact of one organism on another based in the release of a specific compound.
* there is not a direct touch, but rather it is something that will be release to harm neighbors.

What are two examples of the ammensalism relationship?

Antibiotic production

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Bacteriocin production

How does the amensalism production of antibiotics work?

* we can have a fungus that release a compound that can kill the bacteria
* we can also have a bacteria that can release a compound that can kill another bacteria
* most true antibiotics come from streptomyces which is a bacteria.
* Antibiotics are made as a compound that normally kills/destroys/inhibit something that looks different than you.

How does the amensalism production of Bacteriocin work?

* It is very similar to antibiotic but they are compounds made to kill somebody who looks like you but is not you.

Describe competition

* this type of interaction occurs when two organisms try to acquire or use the same resource.
* there are two outcomes one wins and the other is gone, or neither wins and they share.

How does competition in our immune system keep us healthy?

* A lot of bacteria will compete for the same space and when they do this then pathogens cannot bind and therefore they cannot cause infection and disease.
* An imbalance of your normal flora can cause infections and diseases and that is why it is important to properly take antibiotics and be careful with them.

What is an example of competition helping the immune system?

* In the female GI tract we have bacteria and a yeast (candida albicans)
* Candida albicans is always present in the normal flora at a low enough number where it does not cause harm.
* However, if you take an antibiotic and the bacteria but not candida albicans because it is a yeast.
* now candida albicans will grow out of control because the bacteria are not there to compete with it for space. This is what causes UTIs.

Where can you find a microbiome on your body?

everywhere on your body has its own natural microbiome with different microbes and environments.

Is the CNS sterile?

It is thought to be sterile however, there may be some very specific bacteria that grow in your CNS and they are there for protection.

What are Superorganisms?

* We are.
* when gene-encoded metabolic processes of the host become integrated with those of the microbes.
* we have given up some metabolic processes because we have microbes and they can do it for us.
* we do not have all 20 amino acids but rather absorbe them from our gut microbiome who made it for us- we absorb the precursors.

E. coli and streptococci help make what in the gut?

they help make a reducing environment

What us bifidobacteria and how does it help us?

* it is found in breast fed babies and if you have it early on then you are more likely to be healthy.
* Bifidobacteria causes the gut pH to drop (because it does fermentation) which inhibits pathogens from dropping, so it keeps the gut healthy.
* it can synthesize all amino acids.
* we see them used as probiotics.
* we see it in high concentrations when we are young but it decreases as you get older.

What are germ free animals and how are they used.

* they are used to study the effects of microbes, what the goals of the microbes are.
* these animals have 0 microbes and no normal flora.
* they are exposed to highly purified air and they are coming in contact with absolutely nothing.
* we compare them to normal animals to see the differences.

What are some differences that have been found in germfree animals vs. normal animals.

* animals who have a normal flora will make it through the maze a little quicker than those who do not have a normal flora.
* also when you do not have a normal flora, you notice your immune system is weakened there is not as good of a protection as if you were to have a normal flora.

How else are germ free animals used? (one)

* we use them to slowly add one microbe at a time and see what the outcome is.
* for example if they add bifidobacteria and there is a positive reaction they know that it was that one bacteria on its own.
* but usually bacteria are not alone.

What is the Human Microbe project?

* it was initiated december 2007 by the national institutes of health (NIH) and took about 7 years to complete.
* the NIH was interested in idenfying microbe that grow in and on use.
* they found 5 phyla commonly present in most humans.

how was the Human microbe project performed?

As of 2014, the whole metagenomic sequence for about 800 healthy humans cohort samples were obtained

* 16s sequence data from about 5,000 healthy human cohort sample ere obtained.
* they sequenced the data and they placed the data in a little map and found patterns.

What are the 5 phyla that the NIH found commonly present in most humans

* 1. actinobacteria
* 2. Bacteroidetes
* 3. Firmicutes
* 4. Fusobacteria
* 5. Proteobacteria

What are the aspects of the skin which make it an inhospitable environment?

* Slightly acidic pH
* it has a high concentration of NaCl ( salt
* Normally, we have many areas low in moisture on the skin.
* All of these together make it hard for microbes to grow on it but some of them can.

What are some examples of microbes which can live on the skin.

Staphylococcus epidermis

Acne Vulgaris

Candida Albicans

What is acne vulgaris and what does it do?

Acne Vulgaris is cause in part by Cutibacterium acnes.

* when the environment changes on your porse, such as when there is sebum accumulation (imbalance) in a high concentration the bacteria thrives. and when it thrives it causes acne.
* it is an opportunistic pathogen because we can carry it- it only causes harm when it is a part of an imbalance.

What is oleic acid?

it is made by gram-positive bacteria

* C. acnes inhibit the growth of gram negatives

What makes cathlicidins and what do they do?

* They are made by our innate immune cells, macrophages, and granulocytes.

Does the eye have a normal flora?

* it does not have A LOT of normal flora - although it does not contain a lot of bacteria it does contain some

Where on the eye is the bacteria found and what is the most predominant bacteria and where is it found?

* a small number of commensal bacteria is found on the conjunctiva (white part) of the eye


* the bacteria is normally going to be found around the eye
* the predominant bacteria is staphylococcus epidermidis.

What usually happens to your eyes when you have allergies

inflammation and puffiness

what usually happens to your eyes with a viral infection

you normally have lacrimation w

what usually happens to your eyes with a bacterial infection?

you normally have mucus accumulation

What is the flora of the external ear?

it has a normal flora similar to the skin flora but it also has some fungi. and example of a fungi you might see in the ear is Candida auris.

What are somethings that we may have in our mouth that are caused by bacteria?

dental plaque, dental caries, gingivitis, and periodontal disease

What is something that can form on your teeth and destroy them?

biofilms.

What kind of bacteria grow in the mouth?

After teething (once your adult teeth are in) you are going to see a shift in the type of bacteria growing in your mouth from aerobic to anaerobic because it can now grow in between your teeth and on your gum-obligate anaerobes become dominant.

* this is why we treate gingivitis with antibiotics.

Does the stomach have bacteria in it if it does what bacteria?

The stomach does not have a lot of bacteria in it because it is an acidic environment- but it can still have some bacteria in it

* like h. pylori, the causitive agent of ulcers.

How can some bacteria survive the stomachs acidic environment?

They can survive if they are ingested in food particles

* when you eat, you are chewing your food, so food particles can actually protect those microbes as they go through the stomach and then the intestines.

Where is the most diverse and high concentration of bacteria in the body?

Towards the end of the small intestine, you start noticing the pH shifts from acidic to alkaline -- we start with an acidic stomach, go towards neutrality, and finally end in an alkaline environment as you go through the intestines.

* it is in the large intestine

What is the microbiome like in the Duodenum?

there are few organisms here

What is the microbiome like in the Ileum?

* the flora is similar to the colon
* here we see that pH becomes more alkaline
* there are a quite a few of anaerobic Gram-negative bacteria that grow in this lower part of the small intestine and then finally into the large intestines
* Since these are anaerobes any kind of oxygen is being used up as you go trough the intestines
* we also have enterobacteriacae

What is the microbiome like in the large intestine/colon?

* I have the largest and most diverse population of microbes.
* microbes in the large intestine are replaced rapidly because of their high reproductive rate.
* towards the colon there is no oxygen left.
* Coliforms
* we may also have archaea here such as methogens.

What Bacteria is most commonly found in the nose?

Staph aureus and epidermidis

* they are the predominant bacteria
* you will see it just inside your nostrils

The nasopharynx may contain low numbers of what?

It may contain a low number of potential pathogens

* people can carry these pathogens and not get sick just spread them.

What pathogens might be found in the nasopharynx?

Streptococcus pneumoniae

Neisseria Meningitidis

Haemophilus INfluenzae

Where is the oropharynx?

It is the division of the phyrnx lying between the soft palate and the upper edge of the epiglottis

What kind of bacteria grow in the tonsils and where?

* your tonsils are like a sponge so they do have some crypts and holes in them, and there for anaerobes can grow in them
* Anaerobes grow into solar crypts
* if they become too inflamed you get the removed.

What bacteria grow in the oropharynx?

We have gram-positive bacteria (diphtheriods) and Gram-neg cocci

\-we also have these alpha hemolytic streptococci.

Is there a normal microbiota in the lower respiratory tract.

There is no normal microbiota in the lower respiratory tract.

* this is one of the few places in the body that does not have bacteria present -- this is why you have to be very careful with any lower respiratory tract infections.

Why is it important that nothing gets into your lungs?

Since there is not a normal flora in the lungs, anything can attach and replicate very quickly because they have all this space and nutrients with no competition.

How are most microbes kept out of the lower respiratory tract?

* there is a continuous stream of mucous generated by ciliated epithelial cells.
* there are phagocytic action of alveolar macrophages
* Lysozymes in the mucus

How does the mucus in the lower respiratory tract work?

* There is mucus lining your trachea, and that mucus is constantly being removed because you have cilia constantly beating and moving up the mucus- since the mucus is being moved up, we can cough it out, sneeze it out or swallow it.
* the cilia is something that we saw in eukaryotes but not in prokaryotes

How do lysozymes in the lower respiratory tract work?

* we have lysosomes and secreted IGA in your mucus, which will hopefully break down the peptidoglycan organ and neutralize any kind of bacteria or virus.

What are some factors that make the UT tract not favorable for microbes to live in?

* Low pH of urine and the vagina
* The vagina has lactobacilli
* urea and other toxic metabolic end products that are found in urine
* hypertonic nature of the kidney medulla
* constant flushing with urine and mucus that makes it very hard for microbes to stay put, there is a mechanic protection

Does the UT have a normal flora?

the kidneys, ureters, and the urinary bladder are going to be normally free of microbes.

* this also means that if anything makes it to that area, we are in trouble because there is no competition

Where in the UT will you find some bacteria?

* You will have bacteria growing in distal portions of the urethra.
* There is also bacteria growing in the female genital tract.

Describe the flora of the female genital tract.

* females have yeast growing in their vaginas
* the vagina has a complex microbiota in a state of flux due to the menstrual cycle
* there is also a predominant bacteria

What is the predominant bacteria in the female genital tract

Acid tolerant lactobacilli predominate (pH 4.4-4.6)

Why are males less likely to get an infection in their urinary tract?

* they are less likely to get an infection because of the distance barrier of the male urethra
* males have a greater distance between openings and the parts that are more sterile

What is the functional core microbiome

we are becoming more and more accepting to the idea that the gut microbiome is its own organ that we should start treating it, organizing it, and talking about it.

* it is essential to have a core microbiome for homeostasis.

what causes inflammatory bowel disease?

bacteria releasing content that is activating the inflammation in your gut.

What are some roles that microbes play in immunity?

* the normal flora itself is part of innate immunity because it is present and inhibiting others from growing (colonizing)
* Your microbiome is also releasing contents to inhibit the growth of other microbes --these are Bacteriocins
* Your microbiome also plays an important role in keeping the immune system on its toes - constantly having those bacteria present, your immune system is constantly activated

How do antibiotics affect the gut microbial community?

* Antibiotics will change the balance of your normal gut microbiome/normal gut flora.
* taking a 10 day probiotic can change your gut microbe for up to a year.
* unfortunately we do not have that magic bullet that targets only the bad bacteria, but rather they target all bacteria equally.

Microbes release what to target pathogens?

Toxic peptides to target pathogens.

* such microbes include bacteriocins, microcins, and colicins.

What behavioral traits have been connected back to the gut microbiome?

Inquisitiveness, sociability, anxiety, and depression

how does your microbiome have an effect on your immune system?

* Either by its metabolism or its own presence, they are doing something to your immune system .
* that change to your immune system causes changes to your CNS- these changes can be an increase or decrease in inflammation: the presence of cytokines and chemokines
* whatever they are doing is changing the cns

what connects the enteric nervous system to the CNS and how is this important?

he vagus nerve is the nerve that connects from your intestines/gut back to your CNS

There is some signaling pathway that is being activated.