The Human Microbiome - Video Tutorials & Practice Problems
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1
concept
The Human Microbiome
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in this video, we're going to refocus our attention on the human microbiome. And so first we need to recall from some of our previous lesson videos is that the microbiome is also sometimes referred to as the normal flora. And so the microbiome or the normal flora refers to the communities of microbes that grow on and in the bodies of all humans at all times. And so these microbes that are part of the microbiome, or normal flora live in symbiotic relationships with humans and they can be further classified into two groups. They can be classified as resident microbiota or they could be classified as transient microbiota. Now, resident microbiota as its name implies, include microbes that are going to be residing in our bodies for long periods of time. And so the resident microbiota are microbes that are almost always on or in the host for extended long periods of time. Now, the transient microbiota, on the other hand, as its name implies, includes microbes that are only temporarily found on the body for relatively short periods of time. And so of course pathogens, disease causing agents are going to be considered transient microbiota there only on us for relatively short periods of time in most cases, but not in all cases. Now, if we take a look at our image down below, we can get a better understanding of the difference between resident and transient micro biotic and so if we take a look at the left hand side over here, notice it's an image focused on the resident microbiota, which of course are going to be microbes that are almost always on the host for extended periods of time. And so notice here we have a cartoon showing you these microbes that are residing in the lungs, calling the lungs home sweet home. And noticed that saying, I love our home in the lungs. I never want to leave and they seem pretty comfortable and relaxed and they don't look like they're going anywhere anytime soon. And so these resident microbiota are on or in our bodies for long periods of time. Now, on the right hand side, we're focused in on the transient microbiota. And the transient microbiota, of course, are only found in our bodies for temporary periods of time or short periods of time. And so notice that these microbes right here don't look like they're sticking around much longer. Uh They've got their bags packed and they're ready to hop on the microbe transit to make their way to their next destination because they're not going to remain in or on the host for extended periods of time. So notice their next stop is going to be outside of the host. And again, they are going to be temporarily found on the body. And so this year concludes our brief intro to the microbiome and normal flora and our intro to resident and transient microbiota. And we're going to continue to talk more about the microbiota as we move forward in our course. So I'll see you all in our next video
2
Problem
Problem
Scientists commonly call humans 'superorganisms'. What is this description referring to?
a) Humans are the most intelligent and influential organisms on the planet.
b) Each human is an ecosystem for trillions of microorganisms.
c) Humans are the only organisms that determine the success of other organism species.
d) Each human is host to a unique species of microorganism.
A
Humans are the most intelligent and influential organisms on the planet.
B
Each human is an ecosystem for trillions of microorganisms.
C
Humans are the only organisms that determine the success of other organism species.
D
Each human is host to a unique species of microorganism.
3
Problem
Problem
Which of the following answers does not include an example of transient microbiota?
A
Microorganisms that inhabit certain body sites for extended periods of time.
B
Microorganisms that are able to inhabit different body sites during their lifetime.
C
Microorganisms that only occupy the body for a short period of time.
D
Microorganisms that are pathogenic and eventually removed by the body's immune system.
4
concept
Microbiome Composition
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5m
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in this video, we're going to discuss the composition of the human microbiome. And so it turns out that in 2007, the human microbiome project started and the human microbiome project is really just a set of coordinated studies that are all designed to reveal the composition of the human microbiome. And it also aims to study the relationships of the normal flora or the microbiome with various human hosts. And so one of the main goals of the human microbiome project is to understand how changes in the microbiome throughout a person's lifetime can affect that person's health and disease. Now, it's important to note that humans actually start to develop their microbiome at birth. And it turns out that even the birthing method can affect the microbiome. And so uh infants that experienced a vaginal birth will be exposed to different microbes. Um then infants that are birthed through a cesarean birth. Also, breast milk actually contains many beneficial microbes and carbohydrates that are really important for an infant microbiome. Uh and so the feeding method can, and the diet can also contribute to the microbiome. Now, in adults, there are many, many different factors that contribute to the microbiome changes that occur over a person's lifetime. And down below in this image, we're showing you many of the different factors that can contribute to the microbiome. Now, something that's interesting to note, for example, is that the microbiome of obese adults actually differs from the microbiome of lean adults. And so this goes to show that the microbiome can impact things such as obesity. Now, over time, it's important to note that a person's microbiome can change and the person's microbiome changes as they are exposed to or encounter new microbes and new environments. And so a person's microbiome today may be different than their microbiome a year from now, depending on their experiences and the microbes and environments they were exposed to. Now interestingly, here we have that researchers have begun to find a correlation between the microbiome composition and disease. And so it turns out that having an unhealthy microbiome can lead to higher risk of disease. And so, for example, intestinal dis by osmosis, which, despite aosis is a term that refers to an imbalance of the microbiome can actually lead to inflammatory bowel disease. And so by not having an appropriate intestinal microbiome, it could lead to increased risk of inflammatory bowel disease. And so if we take a look at our image down below. Once again, we can see many of the different factors that contribute to the microbiome and again, humans acquire their microbiome at birth. And again, the birthing method can affect the microbiome. The feeding method in terms of breast milk or formula, whether or not the infant or the baby goes to a daycare or a school, a public school or if their home school, they can be exposed to different microbes in different environments. Also genetics can actually play a part in the microbiome as well. Whether or not you have siblings can change the environment and again change the microbes that a person is exposed to different types of infections can also affect the microbiome and make changes in the microbiome, the diet that a person has throughout their lifetime, whether they're eating healthy foods or whether they're eating more fatty foods will affect the type of microbiome that they have uh medications and vaccinations that a person may receive could affect their microbiome the particular season. So in the summertime, in the wintertime, a person's microbiome could change or defer and also habits such as smoking can also impact the person's microbiome, including secondhand smoking as well for infants. And so all of these different factors can contribute to a person either having a healthy microbiome, a balanced microbiome that is appropriate or it could lead to dis by osmosis, which recall that despite aosis once again is an imbalance in the microbiome. And so notice here, there is a lot more of this microbe and much less of this microbe and that creates this imbalance. And the imbalance this dis bios is can lead to increased risk of disease. For example, like we said earlier, intestinal, despite aosis could lead to inflammatory bowel disease. And so notice that this person here is not feeling well because their microbiome is not balanced. And so this here concludes our brief lesson on microbiome composition and we'll be able to get some practice applying these concepts as we move forward in our course and learn more about the microbiome as well. So I'll see you all in our next video.
5
Problem
Problem
Which of the following influences the types and amounts of microorganisms found in and on your body?
A
Your age.
B
Your diet.
C
Your medications.
D
All of the above.
6
Problem
Problem
Recent research suggests that babies born via cesarean section are more at risk for developing allergies. Why might this be?
A
C-sections babies are not exposed to the mother's vaginal microbiota.
B
Early exposure to normal microorganisms of the microbiome will allow a baby's microbiome to form quicker.
C
A less developed microbiome causes an individual to be more sensitive and reactive to allergens.
D
All of the above.
7
Problem
Problem
Newborn babies acquire the microbes of their microbiota by:
A
Passing through the birth canal.
B
Breastfeeding.
C
Contact with their mother's skin.
D
Their environment.
E
All of the above are a source of microbiota.
8
concept
Microbiome Protects Against Infection
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6m
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in this video, we're going to discuss how the human microbiome can protect against infection. And so first we need to recall from some of our previous lesson videos that the microbiome itself is actually part of innate immunity because it can protect against pathogens non specifically. And that's because the microbiome can create a competitive and unfavorable environment for pathogens protecting us from those pathogens. And so some of the microbes of our microbiome can block the attachment sites that pathogenic microbes need to use to colonize the area. And so by blocking these attachment sites, the microbes of the microbiome are preventing pathogenic microbes from infecting us. Now other microbes of the microbiome can also create toxins or toxic substances that are not toxic to us, but they're only going to be harmful and toxic to some pathogenic microbes again, protecting us from those pathogenic microbes. And so if we take a look at our first image down below, notice that it's focused on how the microbiome can protect against infection. And so notice on the left over here, we are showing you a human and you can see all of the different microbes that are part of the microbiota on this human. And then notice that just outside of the human over here are some pathogenic microbes. And so if we zoom into this particular region right here, that's what this boxes, which will notice is that within the human we have the normal microbiota and then on the outside of the human, we have the pathogenic microbes and notice in this cartoon that the normal microbiota are saying you are not welcome here to the pathogenic microbes and the pathogenic microbes are saying, hey, they're blocking all of the attachment sites. And so these pathogenic microbes are not going to be able to colonize the human body because of the normal microbiota blocking the attachment sites and again creating toxins that prevent the pathogenic microbes from infecting us. And so another thing that our microbiome can do is it can actually stimulate the adaptive immune system and it can stimulate the adaptive immune system towards pathogens that we have not even yet encountered. And so how is that possible? How can our normal microbiome protects us from pathogens that we have not yet encountered? Well down below, we're walking you through an example of how this could occur. And so imagine a situation where a small number of skin microbiota actually enter into our tissues via cuts that might be in our skin. And so when these small numbers of skin microbiota into enter into our tissues via cuts our body and our immune system can actually produce antibodies against the skin microbiota. And so these antibodies that were produced against the skin microbiota, they can also be effective against pathogens that have similar antigens to the skin microbiota, ultimately protecting us against pathogens that we have not even yet encountered. And so if we take a look at our second image down below, we can get a better understanding of this idea of how the microbiome can actually stimulate the adaptive immune system. And so notice that in this image we have a cartoon and the cartoon has two scenes, it has a left scene over here which is first and then it has the scene on the right and in the scene on the left which you'll notice is that all of this pink that you see here represents the human body and this here represents specifically the skin. And what you'll notice is that in the skin we have a wound site here, an open wound and notice that we also have our skin microbiome over here that are normal and healthy on our skin. However, when there is a cut, sometimes our microbes of our skin microbiome can make their way into the tissues via the wound site. And so notice here one of the skin microbiome uh cells here is curious and he's saying, hmm, I wonder what's in there. And so notice they make their way into the tissues and our adaptive immune systems such as our B cells, recognize them. Say you shouldn't be here and they start to create antibodies towards the skin microbiota. And so that's the first scene over here now. In the next scene, which you'll notice is that the skin microbiota here is a little bit beat up from going in the first time and notice that the antibodies that were made for the skin microbiota can also be effective against pathogens that have similar antigens to the skin microbiota. And so notice that the skin microbiota here is saying, hey hey, you look just like me, meaning that this skin microbiota looks very similar to the pathogen in terms of its surface antigens. And so he's warning him. The skin microbiota is warning this guy, if you go in there, it's over. And so the pathogen saying, you can't scare me and the pathogen goes into the tissues and realizes that he's made a mistake because there are already antibodies that are effective against him. And so basically what we're seeing here is that our normal skin microbiota can stimulate our adaptive immune system to be effective against pathogens that we have not yet encountered helping to protect us against these pathogens. And so this here concludes our brief lesson on how the microbiome can protect against infection and pathogens. And we'll be able to get some practice applying these concepts as we move forward and learn more as well. So I'll see you guys in our next video
9
Problem
Problem
Which of the following is not a way in which our microbiome helps protect our bodies from pathogens?
A
Microbes of our microbiome create compounds that helps us digest our food.
B
Microbes of our microbiome create compounds that are harmful to pathogenic microbes.
C
Microbes of our microbiome outcompete pathogenic microbes for resources.
D
Microbes of our microbiome block entrances and binding sites in our bodies.
10
Problem
Problem
Certain antibiotics inhibit the growth of Lactobacillus species of bacteria. Adult women who take these antibiotics commonly have vaginal yeast infections following their antibiotic treatments. . Which of the following statements about the Lactobacillus bacteria and yeast of the vagina is false?
A
The yeast is a pathogenic microbe in the vagina.
B
The Lactobacillus bacteria and yeast compete for resources in the healthy microbiome.
C
The antibiotics have caused an imbalance of the bacterial and yeast populations of the vagina.
11
concept
Microbiome Promotes Immune Tolerance
Video duration:
5m
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in this video, we're going to talk about how the human microbiome can actually promote immune tolerance. Now, before we continue, it's important to recall from some of our previous lesson videos that we've already discussed immune tolerance. And so if you don't remember much about immune tolerance, be sure to go back and check out those videos before you continue here. Now, that being said, it's important to note that both T. And B cells must be able to build immune tolerance to our microbiome or towards our normal flora in order for the T. And B cells to avoid attacking our microbiome. And so again, recall from some of our previous lesson videos that immune tolerance can be defined as the ability for our immune system to distinguish between harmless antigens and harmful antigens and immune tolerance is very important for preventing auto immunity or autoimmune diseases which are characterized by our immune system attacking our own healthy cells. Now also recall from some of our previous lesson videos that regulatory T cells or T. Regs cells are important for preventing auto immunity as well. And that's because these regulatory T cells or T rex cells are going to inhibit the activity of other T cells and prevent those other T cells from targeting the hosts microbiome and healthy self cells which again, we do not want our immune system targeting these cells. Now, interestingly enough, it turns out that there are many scientific studies that have shown that early and sufficient exposure to microbes as an infant or child can actually help to increase t rig cell activity or regulatory T cell activity. And that again is going to help prevent autoimmune diseases and can also help to prevent allergies as well. And this directly leads us into what is known as the hygiene hypothesis, which basically states that insufficient exposure to microbes can actually increase a person's risk of developing allergies and autoimmune disorders. And so if we take a look at our image down below, we can get a better understanding of both the hygiene hypothesis and how the microbiome can help to promote immune tolerance. And so notice that this image is broken up into a top half here with a yellow background and the bottom half here with a pinkish background. And what you'll notice is that on the far left over here, we're showing you an infant or a child here who has exposure to many microbes as an infant. So you can see the diversity of microbes that this infant is exposed to and being exposed to so many different microbes at a young age can help too create high regulatory T cell activity. And so notice that there are many regulatory T cells with high activity. And again, recall that the regulatory T cells like this cartoon is trying to display. They are important for inhibiting the activity of other immune cells to prevent them from attacking the healthy microbiome and healthy cells cells. And so notice over here, we're showing you these immune system cells that are looking to destroy the microbes. However, the regulatory t cells says stop only destroy the pathogens. And so it's preventing an immune response towards the healthy microbiome and helping to redirect the immune cells to target the pathogens only. And so with high tier egg cell activity, the immune system is able to build a tolerance uh for the microbiome, tolerating the microbiome so that it is not targeted and only attacking the dangerous pathogens. Now on the bottom left over here, we're showing you an infant or baby that is having exposure to a few very few microbes as an infant. And so notice that here we only have very few microbes in comparison to all of these microbes the top baby is exposed to. And so having very few microbe exposure as an infant or child will lead to relatively low regulatory T cell activity or T rex activity. And so notice here that we have a relatively low number of these tier egg cells. And so under these conditions, the immune system is going to be at higher risk of lacking tolerance towards the microbiome. And so that can lead to increased risk of allergies as well as increased risk of autoimmune disorders. And so once again noticing this cartoon, we're showing you the immune system cells looking to target these microbes and notice that with low regulatory T cell activity it will not be able to inhibit these immune cells in the way that they should. And so notice here that the T rex is saying I can't tell the difference between them anyways. But ultimately it's just that these T rex sell these immune system cells here will be targeting both the healthy mike o'brien as well as the pathogens and again that could lead to potential allergies and autoimmune disorders. And so this year concludes our brief lesson on the microbiome and how it can promote immune tolerance. And uh we also discuss a little bit about the hygiene hypothesis here and so we'll be able to get some practice applying these concepts as we move forward in our course. So I'll see you all in our next video.
12
Problem
Problem
The "hygiene hypothesis"proposes that during childhood:
A
Lack of exposure to microbes can promote development of allergies.
B
Hand washing prevents against most dangerous infections.
C
The immune system develops best in a clean environment.
13
concept
Microbiome Makes Nutrients & Aids in Host Digestion
Video duration:
3m
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in this video, we're going to talk about how members of our normal microbiome can actually make nutrients for the host and aid and host digestion as well. And so once again, an important feature of the microbiome is its ability to produce essential nutrients for the host. And so down below we have three examples of how the microbiome can either make nutrients for the host or aid and host digestion. And so intestinal microbiome members can actually produce essential vitamins that are critical for the host. For example, vitamins B and vitamin K. That can be absorbed and utilized by the host. Also, intestinal microbiome members can also produce enzymes that are capable of degrading complex carbohydrates for the host, essentially aiding and host digestion helping the host break down complex carbohydrates so that the host can utilize the smaller segments of those carbohydrates. And then last but not least here were also mentioning how fermenting bacteria that are part of the normal microbiome can also produce energy sources for epithelial cells. And so if we take a look at our image down below, we can get a better understanding of how the microbiome can once again make nutrients for the host and aid in digestion. And so notice over here, we're showing you a human and we're zooming in specifically to the gut region here and within the guts. You can see that there are going to be many microbiome, many microbes that are part of the microbiome. And so the microbes of the large and small intestine here which will notice here, we have these blue microbes that are producing vitamin B. And here this microbe is producing vitamin K. And so we can label this as vitamins that are being produced by members of the microbiome. And then of course the host can utilize these essential critical vitamins for its own use. Down below. Over here, on the bottom left of our image, we're showing you how some of the members of the microbiome can actually produce enzymes represented here as these little tiny scissors. And these enzymes are capable of degrading complex carbohydrates into smaller components and that is going to aid in digestion. And so these enzymes can degrade these complex carbohydrates for the host. And then last but not least here. We're also showing you some fermenting bacteria here that are capable of producing energy sources that can be utilized by epithelial cells, allowing them to obtain energy. And so ultimately the big takeaway here is that the normal microbiome plays a critical role in making nutrients for the host and aiding and host digestion. And once again, without the members of the normal microbiome life, as we know, would not be able to exist. And so we rely on our microbiome to create nutrients and to aid in our digestion. And so this here concludes our brief lesson on this. And we'll be able to get some practice applying this as we move forward. So I'll see you all in our next video
14
Problem
Problem
Which of the following is true about how the microbes of our microbiome help maintain our health?
A
They block pathogen attachment to host cells.
B
They establish competition for available nutrients and vitamins.
C
They produce antimicrobial substances that damage pathogenic microbes.
D
They stimulate the immune system to attack pathogenic microbes.
E
All of the choices are true.
15
Problem
Problem
Humans do not possess the enzymes required to break down most dietary fibers found in whole grains, beans, and vegetables. However, some fiber can be digested in our guts. How does this happen?
A
Certain bacteria in our gut microbiome digest the fiber in our food and provide us with nutrients.
B
Certain yeasts in our gut create vitamins which help break down fiber in our food.
C
Certain bacteria in our gut induce our intestinal epithelial cells to create enzymes which can break down fiber.
