Enteric and Skin Infections Overview

Congratulations to getting to the part of the semester where we have done most of the heavy lifting. We've learned about metabolism, we've learned about genetics, and we've learned about the immune system. Those are the three biggest, hardest, most complex pieces that we cover in microbiology. For the remainder of this semester, we're going to be focusing on different areas of the body and the kinds of diseases that we see. Some of these are diseases we've already covered in detail in our Disease of the Day series, and so I'll give them a mention here to put them in context. Other diseases that we don't cover in Disease of the Day, I'll spend a few more minutes on, but we're going to be working through some of the major epidemics that we see on Earth right now, including things like TB and HIV and influenza, etc., in this set of... diseases that we're going to talk about in the last few weeks of class. Today what I want to do is cover generally enteric and skin infections. Most of these pathogens we have covered in detail in Disease of the Day. So we're going to use this time to talk about the specific ways that your body protects itself from enteric and skin infections and kind of categorize these diseases into groups to try to organize them in a cohesive way. I hope you enjoyed this first video that I put up on the death of three U.S. presidents being linked to drinking water in the White House. I find it pretty entertaining, and it's always fun to think about this, and then sometimes you'll hear on the news about people promoting raw water, untreated water as being more nutritious and healthier, which is crazy. Here's an example of why it's actually not just not nutritious, but just downright dangerous. You figure the president, even in the 1840s, was getting the best that they had in terms of health care and sanitation. When you have three of them in a row dying of waterborne diseases, you know things are bad. Here's to the San Francisco Water Department and our fabulous, Hetch Hetchy water that's treated to make it safe to drink. There is a fantastic video that I put on to the homework. It's a nature video. Nature is a scientific journal. If you're not familiar with it, it's really well respected. It does a great job talking about the immunology of the gut. And I'm not going to recapitulate that here, but I will put a link to the video in this video here on this slide for you to see. It doesn't hurt to go back and listen to this again. I learn things each time. Bye. Listen to it. It's a really well done. You don't need to know everything in as much detail as they go into in this video But I do want you familiar with it on the next exam. What are some of the take-home messages for your GI tract? Well, the reality is is that you eat food and drink water and you are exposed to a lot of microorganisms through the GI tract and so the GI tract is Special it has more immune cells than any other part of your body The surfaces of the GI tract are coated with mucus that's going to prevent pathogens and commensals from getting through the gut lining into your body. You have IgA, which is that secreted antibody that's on most of these intestinal surfaces. And you have peristaltic movement. So the smooth muscle of your gut is constantly moving things through. So you put things in your mouth, they leave the other end. And that... They don't sit in your gut. They're constantly being moved through your gut. There are secretions. So for example, saliva, we said in the past, contains that enzyme lysozyme, which breaks down peptidoglycan. It also contains another protein called lactoferrin, which binds up iron that bacteria need to survive. We've talked about your stomach acid. Hydrochloric acid is a very, very inhospitable. place for bacteria to be. And so the first thing they hit when they get into you is your stomach. That's going to kill a large number of any potential pathogens right there. And then when they get past your stomach, they get exposed to bile in your small intestine. And bile itself is antimicrobial. Remember that some of the media that we used this semester to grow bacteria that were only gram-negative contained bile in it, right? Things like hectoplasm. doing for example because bile itself will kill quite a few microorganisms. So your GI tract built in lots of ways to limit the exposure of these microbes that are in your food to getting further inside your body. Now this is where that video that I had in the homework is really helpful. So one of the things they talk a lot about is the structure of the GI tract as well as these structures called Peyer's patches which are in the small intestine. And we know that Peyer's patches do a couple of things. One of the roles that they play in the cells that are there and there's B cells and T cells and dendritic cells and macrophages so there's a whole host of these immune cells. They sample microbes as they're coming through your gut. And actually, the Peyer's patches play a really important role in tolerance so that your body doesn't overreact to these pathogens. In a way, you're training your gut and your immune system to say, hey, these are our old friends. They're part of our digestive system. They belong here. This is an ecosystem, and we're not going to attack them. So the Peyer's patches both play a role doing that, as well as when a pathogen is present and begins to do damage to the intestine, the PEARS patches, the same cells can then ramp up to actually stimulate an inflammatory response. And what we don't want to see in the gut is sustained inflammatory responses that result in things like Crohn's disease or irritable bowel syndrome, etc. All right, so that's this video. And we talk about GALT, this gut-associated lymphoid tissue. We're talking a lot about these PEARS patches. Don't forget that you also, in your mouth, or closer to your mouth, you have tonsils and adenoids. These, we believe, have GALT. We used to just take people's tonsils out almost as a rite of passage of childhood. We don't do that now. And then another thing that was not mentioned in the video but very important to remember is that these commensal bacteria have other strategies themselves to protect them from your immune system, including coating themselves with sugar molecules. so that they don't look dangerous. So it's almost like wearing a disguise. And this will help them survive your immune system. And it's an interplay between your immune system and these microbes. Many of these commensal microbes, if they did get into you, can cause illness. It would be an opportunistic infection. So there's a balance between protecting your body from them invading you, but also allowing them to live at peace in your GI tract to fulfill the role of a commensal organism. So there are about 600 species of bacteria just in your mouth. 600 species, that's not how many bacteria, that's how many different kinds of bacteria. Your stomach contains transients primarily, but there are also some residents. And then your large intestine is where the big numbers really go up. So we get in every part of the intestine, the numbers increase until you get to the colon, and there's about 10 to the 11 bacteria. per gram of stomach contents. And this talks a little bit about some of the protective functions just in your GI tract. So you have just the fact that you have the commensal bacteria that's going to displace pathogens that might be there. The bacteria also compete for nutrients, so that's going to make it harder for a pathogen to get going. They compete for sites where they might bind to actually colonize. And then these bacteria are... of course undergoing microbial antagonism so there's a certain amount of chemical warfare between these organisms and hopefully if you have a nice healthy gut with lots of good commensal bacteria they're going to win these wars because they're going to be in abundance and no pathogen will really have a chance you also have the iga that's present in your gut that's going to to help uh prevent uh bacteria by neutralizing them prevent bacteria from causing problems um You have a metabolic function. So, for example, the bacteria that are there do a lot of good things for you. They're going to synthesize some of your vitamins. All right. So they're going to ferment some of the dietary food that your body can't ferment and allow you to get some energy from that. So there's a nice relationship between these bacteria that are in your gut and your gut itself, its function, and its ability to withstand the invasion of a pathogen as well. This slide is just for your information. You can go back and take another look at it. A couple of key points. One is that the further you get into the gut, the larger the number of bacteria, with the exception of the stomach. But once you get into the small intestine, you can kind of see the various parts of the small intestine. You see these numbers kind of increase until you get to the colon where you have the really big numbers. So bacterioides, the fetobacterium, clostridium. um fecalibacterium, streptococcus, you know, lots of different organisms that we see in your gut. And we really, a lot of work has been done in the last, I want to say 10 years to actually begin characterizing the microbes that are in the gut to get a better sense of which ones are present in people with healthy guts, people who don't have things like irritable bowel disease versus people who might have some pathogenesis of their gut. Maybe they're more sensitive to autoimmune diseases, for example, maybe that they're more sensitive to getting opportunistic infections, etc. You know, how do the different species present in your gut contribute to these diseases? It's an area of a lot of inquiry, and it's a fun one to watch, and hopefully in a few years we'll know more and maybe have some legitimate, you know, probiotic treatments beyond fecal transplants that we can use to help people who are struggling with some of these. chronic inflammatory diseases of the bowel. This is a wonderful article from the New York Times. It's about two years old now. I will put a link to the article. This really talks just to this idea. Your mom has told you, right, you hear about it on the news all the time, fiber is good for you, eat more fiber. So we've always been able to associate fiber with things like regularity in terms of bowel movements. and health as well. People who eat more plant-based foods tend to be healthier. So there's some evidence now that we understand more why, and this has to do with something called a prebiotic function, which is by having more fiber in your diet, you seem to be feeding the bacteria that support better health. So you're providing those bacteria with good nutrition as opposed to feeding bacteria that are going to be more prone to be associated with inflammation, for example. So great article. makes a lot of sense that, you know, one of the reasons you should eat a varied, healthy, plant-based diet is actually because you're not just taking care of yourself, but you're taking care of these commensal organisms living in your gut. All right, so that's a little bit on the commensal organisms in your gut, the good things they do for you, your immune system, and how that functions in the GI tract. Next, we're going to talk about when things go wrong and discuss infectious disease in the gut specifically.

Some of these are diseases we've already covered in detail in our Disease of the Day series, and so I'll give them a mention here to put them in context. Other diseases that we don't cover in Disease of the Day, I'll spend a few more minutes on, but we're going to be working through some of the major epidemics that we see on Earth right now, including things like TB and HIV and influenza, etc., in this set of... diseases that we're going to talk about in the last few weeks of class.

Today what I want to do is cover generally enteric and skin infections. Most of these pathogens we have covered in detail in Disease of the Day. So we're going to use this time to talk about the specific ways that your body protects itself from enteric and skin infections and kind of categorize these diseases into groups to try to organize them in a cohesive way.

I hope you enjoyed this first video that I put up on the death of three U.S. presidents being linked to drinking water in the White House. I find it pretty entertaining, and it's always fun to think about this, and then sometimes you'll hear on the news about people promoting raw water, untreated water as being more nutritious and healthier, which is crazy. Here's an example of why it's actually not just not nutritious, but just downright dangerous. You figure the president, even in the 1840s, was getting the best that they had in terms of health care and sanitation. When you have three of them in a row dying of waterborne diseases, you know things are bad.

Here's to the San Francisco Water Department and our fabulous, Hetch Hetchy water that's treated to make it safe to drink. There is a fantastic video that I put on to the homework. It's a nature video.

Nature is a scientific journal. If you're not familiar with it, it's really well respected. It does a great job talking about the immunology of the gut.

And I'm not going to recapitulate that here, but I will put a link to the video in this video here on this slide for you to see. It doesn't hurt to go back and listen to this again. I learn things each time.

Bye. Listen to it. It's a really well done. You don't need to know everything in as much detail as they go into in this video But I do want you familiar with it on the next exam.

What are some of the take-home messages for your GI tract? Well, the reality is is that you eat food and drink water and you are exposed to a lot of microorganisms through the GI tract and so the GI tract is Special it has more immune cells than any other part of your body The surfaces of the GI tract are coated with mucus that's going to prevent pathogens and commensals from getting through the gut lining into your body. You have IgA, which is that secreted antibody that's on most of these intestinal surfaces.

And you have peristaltic movement. So the smooth muscle of your gut is constantly moving things through. So you put things in your mouth, they leave the other end.

And that... They don't sit in your gut. They're constantly being moved through your gut. There are secretions. So for example, saliva, we said in the past, contains that enzyme lysozyme, which breaks down peptidoglycan.

It also contains another protein called lactoferrin, which binds up iron that bacteria need to survive. We've talked about your stomach acid. Hydrochloric acid is a very, very inhospitable. place for bacteria to be.

And so the first thing they hit when they get into you is your stomach. That's going to kill a large number of any potential pathogens right there. And then when they get past your stomach, they get exposed to bile in your small intestine. And bile itself is antimicrobial. Remember that some of the media that we used this semester to grow bacteria that were only gram-negative contained bile in it, right?

Things like hectoplasm. doing for example because bile itself will kill quite a few microorganisms. So your GI tract built in lots of ways to limit the exposure of these microbes that are in your food to getting further inside your body.

Now this is where that video that I had in the homework is really helpful. So one of the things they talk a lot about is the structure of the GI tract as well as these structures called Peyer's patches which are in the small intestine. And we know that Peyer's patches do a couple of things. One of the roles that they play in the cells that are there and there's B cells and T cells and dendritic cells and macrophages so there's a whole host of these immune cells. They sample microbes as they're coming through your gut.

And actually, the Peyer's patches play a really important role in tolerance so that your body doesn't overreact to these pathogens. In a way, you're training your gut and your immune system to say, hey, these are our old friends. They're part of our digestive system.

They belong here. This is an ecosystem, and we're not going to attack them. So the Peyer's patches both play a role doing that, as well as when a pathogen is present and begins to do damage to the intestine, the PEARS patches, the same cells can then ramp up to actually stimulate an inflammatory response.

And what we don't want to see in the gut is sustained inflammatory responses that result in things like Crohn's disease or irritable bowel syndrome, etc. All right, so that's this video. And we talk about GALT, this gut-associated lymphoid tissue. We're talking a lot about these PEARS patches. Don't forget that you also, in your mouth, or closer to your mouth, you have tonsils and adenoids.

These, we believe, have GALT. We used to just take people's tonsils out almost as a rite of passage of childhood. We don't do that now. And then another thing that was not mentioned in the video but very important to remember is that these commensal bacteria have other strategies themselves to protect them from your immune system, including coating themselves with sugar molecules. so that they don't look dangerous.

So it's almost like wearing a disguise. And this will help them survive your immune system. And it's an interplay between your immune system and these microbes.

Many of these commensal microbes, if they did get into you, can cause illness. It would be an opportunistic infection. So there's a balance between protecting your body from them invading you, but also allowing them to live at peace in your GI tract to fulfill the role of a commensal organism.

So there are about 600 species of bacteria just in your mouth. 600 species, that's not how many bacteria, that's how many different kinds of bacteria. Your stomach contains transients primarily, but there are also some residents.

And then your large intestine is where the big numbers really go up. So we get in every part of the intestine, the numbers increase until you get to the colon, and there's about 10 to the 11 bacteria. per gram of stomach contents.

And this talks a little bit about some of the protective functions just in your GI tract. So you have just the fact that you have the commensal bacteria that's going to displace pathogens that might be there. The bacteria also compete for nutrients, so that's going to make it harder for a pathogen to get going.

They compete for sites where they might bind to actually colonize. And then these bacteria are... of course undergoing microbial antagonism so there's a certain amount of chemical warfare between these organisms and hopefully if you have a nice healthy gut with lots of good commensal bacteria they're going to win these wars because they're going to be in abundance and no pathogen will really have a chance you also have the iga that's present in your gut that's going to to help uh prevent uh bacteria by neutralizing them prevent bacteria from causing problems um You have a metabolic function. So, for example, the bacteria that are there do a lot of good things for you. They're going to synthesize some of your vitamins.

All right. So they're going to ferment some of the dietary food that your body can't ferment and allow you to get some energy from that. So there's a nice relationship between these bacteria that are in your gut and your gut itself, its function, and its ability to withstand the invasion of a pathogen as well.

This slide is just for your information. You can go back and take another look at it. A couple of key points. One is that the further you get into the gut, the larger the number of bacteria, with the exception of the stomach.

But once you get into the small intestine, you can kind of see the various parts of the small intestine. You see these numbers kind of increase until you get to the colon where you have the really big numbers. So bacterioides, the fetobacterium, clostridium. um fecalibacterium, streptococcus, you know, lots of different organisms that we see in your gut.

And we really, a lot of work has been done in the last, I want to say 10 years to actually begin characterizing the microbes that are in the gut to get a better sense of which ones are present in people with healthy guts, people who don't have things like irritable bowel disease versus people who might have some pathogenesis of their gut. Maybe they're more sensitive to autoimmune diseases, for example, maybe that they're more sensitive to getting opportunistic infections, etc. You know, how do the different species present in your gut contribute to these diseases? It's an area of a lot of inquiry, and it's a fun one to watch, and hopefully in a few years we'll know more and maybe have some legitimate, you know, probiotic treatments beyond fecal transplants that we can use to help people who are struggling with some of these.

chronic inflammatory diseases of the bowel. This is a wonderful article from the New York Times. It's about two years old now. I will put a link to the article.

This really talks just to this idea. Your mom has told you, right, you hear about it on the news all the time, fiber is good for you, eat more fiber. So we've always been able to associate fiber with things like regularity in terms of bowel movements. and health as well.

People who eat more plant-based foods tend to be healthier. So there's some evidence now that we understand more why, and this has to do with something called a prebiotic function, which is by having more fiber in your diet, you seem to be feeding the bacteria that support better health. So you're providing those bacteria with good nutrition as opposed to feeding bacteria that are going to be more prone to be associated with inflammation, for example. So great article. makes a lot of sense that, you know, one of the reasons you should eat a varied, healthy, plant-based diet is actually because you're not just taking care of yourself, but you're taking care of these commensal organisms living in your gut.

All right, so that's a little bit on the commensal organisms in your gut, the good things they do for you, your immune system, and how that functions in the GI tract. Next, we're going to talk about when things go wrong and discuss infectious disease in the gut specifically.

Transcript for:Enteric and Skin Infections Overview

Transcript for:
Enteric and Skin Infections Overview