The Human Microbiome Project is a $173 NIH funded effort to to discover and study the microbes that live on and in humans. This article from Popular Science discussess the skin microbiome and specifically how the bacteria living on us relate to allergies, asthma, and eczema. Read the article and comment below in regard to at least two of the following:
1. Describe the relationship/number of bacteria to different parts of the skin.
2. Describe the study methods that were used to study the link between allergies, inflammation, and the microbiome.
3. Describe the role of metagenomic analysis is being used to study the skin microbiome.
http://www.popsci.com/science/article/2011-02/our-body-ecosystem-understanding-interplay-between-man-and-microbe
1.Describe the relationship/number of bacteria to different parts of the skin.
ReplyDelete- According to the article bacteria is specific with respect to the area of the body it inhibits. An example mentioned in the article to clearly convey this fact is that a person will not find bacteria that is usually around his or her knee anywhere near their arm. As a result to this specificity, humans will find the same bacteria when comparing the same areas of the body. For instance, if two people were to compare the bacteria behind their ears both should find around 15 of the same species. However, if one took a sample swab of the area behind their ear and the other of their forearm, one would find 15 species while the other would find about 44. In summation, the article states, “…The bacteria are finely tailored to specific locations on the body, rather than to individual humans.”
2.Describe the role of metagenomic analysis is being used to study the skin microbiome.
-As mentioned during a previous class lecture, the structure helps understand the function. Metagenomics allows scientists to study an organism's genetic material, proteins and the protein’s pathways. Therefore, understanding the genetic structure of the bacterium will help understand the biological function of the genes as it relates to anything, including the skin. With information as to how it works, a scientist can hypothesize what the bacterium does and the role it plays in causing/enhancing a disease, illness and, in the article’s case, eczema. In the article, researcher Serge mentions that with metagenomics, “[they will know whether] bacteria associated with eczema are the cause of the disease or simply a consequence of living with it." Based on the information attained through metagenomics, it would be safe to assume that studying the metagenomics of bacteria will help to hypothesize on certain aspects that otherwise would be nearly impossible to understand.
1. Describe the relationship/number of bacteria to different parts of the skin. The article states that the epidermal ecosystem is very divers. That is “bacterial populations ranging in size fro m 15 species behind the ear to 44 on the forearm.” Scientists have found that bacteria are tailored to specifis areas on the body, and that the microbiome is not consistent across individuals, but instead to individual humans.
ReplyDelete2. Describe the study methods that were used to study the link between allergies, inflammation, and the microbiome. The study methods were done by a few researchers from the U.S. France, Ireland, and the U.K. They found that half of the people with eczema have mutations in filaggrin, which is a protein in the skin barrier. Researchers think that the flaw in the skin barrier will allow particles to enter the body which will then trigger the immune response. To discover the link between the skin barrier and microbes, researchers will sample Jake and other kids with eczema at three different stages. The first is during a normal period, the second during a flare, and the third is two weeks after treatment. It is unknown whether bacteria associated with eczema are the cause of this disease. Researchers will look at the biological functions of genes and what kinds of proteins they make, it is believed that there is an interdependency among these organisms because they are highly dependent on each other for their survival.
1. Describe the relationship/number of bacteria to different parts of the skin.
ReplyDeleteWe know that the body is made up of trillions of cells. As a result of Leeuwenhoek’s microscopic discovery, curiosity of bacteria has prompted scientists over the years. Now, scientists suspect that there may be a correlation amongst different bacteria and their interactions. Furthermore, research has shown that a different bacterium inhabit various areas of the skin. For example, there is not the same bacterium that covers the skin. There may be one type in skin behind the knees and another type on the crease of the nose. According to Our Body the Ecosystem: Understanding the Interplay between Man and Microbe, studies have shown that there are possibilities of changing bacteria in relation to changing skin flora, which may influence the immune system. In this study frequent sample of skin are taken to measure and evaluate the level (number) of bacteria and if it affects or causes an inflammatory response, disease or severe rashes. Another study lead by Martin Blaser has taken skin samples from the forearms healthy individuals and individuals with Psoriasis. Results concluded that there was an alarming higher number of bacterium in the patients with Psoriasis than the healthy patients. The microbe research being performed can lead to new knowledge of disease, illness, treatment and prevention.
3. Describe the role of metagenomic analysis is being used to study the skin microbiome.
Metagenomic analysis is the observation of the biological function of each genes and what proteins it is made up of. It helps us understand the function which can lead to help scientists understand the structure. In doing so this could reveal the reason why a bacteria is present; as a result of a disease or the cause of disease. Metagenomic analysis is a very complicated process. The results from the analysis can be used to assist with information for the skin microbiome project.
2. The first method of study was putting the skin samples in a freezing temperature, defrosting them, and then extracting the DNA from bacterial cells breaking down bacterial cell walls with an enzyme called lysozyme. Then, the biologist (Deming) uses the polymerase chain reaction (PCR) to make millions of copies of the bacterial gene 16S. DNA sequence is different on different kinds of species of bacteria, so then DNA is amplified and left with a new set of tubes containing the 16S gene. Some biotechnology comes in place where a machine reads “1,500 odd-letters in each 16S fragment, giving the chemical structure of each species.” And finally the sequence data is sent to an internal network for microbiologists can study the link between allergies, inflammation, and the microbiome.
ReplyDelete3. “During a metagenomic analysis, scientists compare thousands of genes present in a particular species’s DNA. By looking at the biological function of the genes—what kinds of proteins they make and what kinds of biological pathways those proteins are involved in—the scientists can make educated guesses about the role of each species, and how different species may work with one another and with our own genome.” And just like Blaser’s father psoriasis case, he noticed that a certain type of medicine interfered with the synthesis of DNA, it killed or almost stopped the bacteria from growing. So metagenomics can help the process of knowing what kind of bacterial interactions with the skin and the genome causes what, if any, disease much quicker.
1) We have ten times the number of bacterial cells in or on the human body in comparison to the trillions of cells we are made up of. I have microbial communites that are found on half a dozen body sites. This includes gut, mouth, skin, and groin. These were the sites use to compare normal patients with patients with medical conditions.
ReplyDelete2)Skins cells are stored at -112F, defrosts tubes, add lysozyme which breaks down bacterial cell walls; shakes concoction using vortex mixer,this releases dna from bacterial cells that float in liquid, pours over gel which leaves bacterial dna fragemtns separated by plymerase chain reaction to make copies of gene 16s.
3)scientists compare thousands of genes present in a particular species DNA by looking at the biological functions of the genes and what kinds of biological pathways those proteins are involved in. The scientist can make educated guesses about the role of species may work with one another with our our genome.
1. The articles sates that there are 10 times more bacterial cells housed by the body than our own cells (in the trillions). There tends to be less bacterial diversity on oily skin areas such as the upper back and around the nose. Dryer areas such as the buttocks and forearm have more species, however are harder to grow cultures from.
ReplyDelete2. Skin samples are taken from patients afflicted with these problems and stored for sequencing later. They have noticed that patients suffering from inflammation and eczema have a mutation in the skin barrier, which allow entry of particles that then trigger an immune response. This may create an environment for other microbes to grow more easily, thus causing symptoms.
3. Scientists now suspect that they are linked through the bacteria on the skin and the balance they have with each other and the human host. That if the bacterial flora gets interrupted somehow than it causes symptoms of eczema and allergies. The Human Microbe Projects is attempting to sequence the genes of the most common bacteria, fungi, protozoa, and viruses to see how they behave and interact with one another.
Melissa Gregory
1. Scientists have found there are 10 times more bacteria on and within our bodies than the 1 trillion cells our bodies are made of. These bacteria reside in different parts of our bodies; gut, mouth, skin, and groin, depending on the environment which they are tailored to thrive within. The article examines how advances in DNA sequencing research have enabled scientists to better understand the relationships between different types of bacteria, fungi, protozoa, and viruses living on our skin, and our immune system interaction to these microbes. As in the case of Jake Harvey, the 14 year old boy from the article, who has been plagued by allergies, asthma, and eczema for most of his life this research could someday provide relief from the symptoms associated with our skin dwelling microbe partners. As cases of asthma, eczema, and hay fever increase throughout the world The Human Microbiome Project could lead to cures for these immune related diseases that affect so many. The skin and its dwelling microbe create an intricate ecosystem that interacts together. These microbes flourish on different areas of the body, such as in the case of eczema affecting the back of the neck, elbows, and back of the knees more prominently. Researchers studying eczema can culture bacteria from patients during different times to determine the interaction these microbes have with our immune system. Through use of polymerase reactions researchers can culture these bacteria in the laboratory to help better understand the genetics sequencing of such microbes in hopes of developing drugs to prevent immune responses. Some finding have shown that the bacteria responsible for eczema may overpopulate the affected area of the skin during an outbreak leading to the itchy dry rash most commonly associated with eczema. Although the sheer number of microbes populating our skin make it more challenging to study than even the Human Genome Project, characterizing microbes and understanding their DNA will help improve the quality of life for people affected by these epidermal dwellers.
ReplyDeleteFirst I would like to say this was a very interesting article. I have a couple of friends whom still suffer from eczema not knowing that the skin diseases lead to more body discomfort. I remember my friend coming to basketball practice and she had mentioned that the eczema was bothering her. I could see some rashes on her legs; they were on the back side of her knees. The rash was very red, and I remember her always having allergies. This article defiantly explains how allergies and eczema go hand in hand with one another. I didn’t realize how disgusting this disease is. It’s unfortunate that people have to suffer from the three most irritating sensations, itching, allergies, and dirty. I would feel so gross if this was me. And due to the fact that some individuals have no control over this condition is very sad. The article mentioned the little boy sleeping with his legs in the air so he can scratch them faster, and having to take a bleach bath, gross. Luckily researchers have found this to be an uprising problem in the world, and they are planning to actually help, and understand why these conditions occur. It seems that the disorder of eczema lives in the creases of our hands, knees, back of our necks and elbows etc. They mention that bacteria live in dry areas. Some projects that have risen to help treat eczema are, “the Human Microbiome Project, researchers plan to characterize the vast numbers of bacteria, fungi, protozoa and viruses in our body by sequencing their genes. That won’t be easy. In the past, researchers had to grow each species outside the body before they could identify it, a process that required intense research to determine optimum growing conditions” (2) some study methods used were swabbing the young man whom didn’t shower. They swabbed his nose, elbow, and knees. They also swabbed perfectly normal people to understand the difference. The article mentioned, “The average human body is made up of trillions of cells. The average human body also houses about 10 times that number of bacterial cells” (1), and this is normal people. Imagine people whom don’t take showers or actual homeless people. Now that’s something to think about.
ReplyDelete1. Describe the relationship/number of bacteria to different parts of the skin.
ReplyDeleteThe articles states that there are 10 times more bacterial cells housed by the body than our own cells. Scientists also stated in the article that bacteria are specific to the area it affects. When taking swabs of two patients from the same area they should find about the same amount of bacteria. But, if one took a sample swab of the area behind their ear and then another on their forearm, one would find 15 species while the other would find about 44.
2. Describe the study methods that were used to study the link between allergies, inflammation, and the microbiome.
Skin samples are taken from patients involved with these things and then stored for later work. In a study they found that patients suffering from inflammation and eczema have a mutation in the skin barrier, which may allow entry of particles that then trigger an immune response. This may create an environment for other microbes to grow more easily, thus causing symptoms.
3. Describe the role of metagenomic analysis is being used to study the skin microbiome.
Metagenomic analysis of the samples is used to find out if bacteria associated with things such as eczema are the cause of this disease. “During a metagenomic analysis, scientists compare thousands of genes present in a particular species’s DNA. They look at the biological function of the genes—what kinds of proteins they make and what kinds of biological pathways those proteins are involved in—the scientists can make educated guesses about the role of each species, and how different species may work with one another and with our own genome” (Hughes).
As someone who has dealt with eczema my whole life this was a very interesting article to read.
ReplyDelete1. Describe the relationship/number of bacteria to different parts of the skin.
The average human body is made up of trillions of cells. The relationship of bacteria to different parts of skin is that the bacteria that is found on one part of the body is different than the bacteria found on a different part of the body.
2. Describe the study methods that were used to study the link between allergies, inflammation, and the microbiome.
The methods that were used to study the link between allergies, inflammation, and the microbiome was that skin cells were taken from different parts of the body and then frozen. After they're unfrozen a biologist adds lysozyme and mixes it with a vortex. When the DNA is released from the cell he pours it into a gel filter looking for a specific gene: 16S.
1. Describe the relationship/number of bacteria to different parts of the skin.
ReplyDeleteThe Human Microbiome Project (HMP) has found that they are thousands of different types of species of bacteria living on the skin. Some areas like behind the ear have as many as 15 different species and the forearm has as many as 44 different types of species. Oily regions of the body tend to have less different types of bacteria where dryer parts may have more.
2. Describe the study methods that were used to study the link between allergies, inflammation, and the microbiome.
Jake, the young patient, has eczema and asthma. First Jake is asked many detailed questions concerning his behaviors. He was also asked not to bathe for 24 hours and not to use his inhaler or any other medications. Samples of Jake's skin are taken in different areas with sterile swabs and scalpels. The samples are stored in a large freezer then lysozyme was used to break down the cell walls of the bacteria and seperates the DNA. The DNA can then be analyzed.
3. Describe the role of metagenomic analysis is being used to study the skin microbiome.
By using metagenomic analysis, scientists can study and understand the different species living on our skin and how it relates to disorders like eczema and psoriosis. They can create a base line for normal people, then look at someone like Jake and compare the differences of their skin's bacteria. This can then help doctors to treat these disorders by understanding what bacteria are not right on the skin.
Jackie Edwards
1. the relationship/ number of bacteria to the different parts of the skin are that there are trillions of cells in the human body. And we have about 10 times the number of bacteria cells and there are 3000 different kind of bacteria speices. There are 15 speics behind the ear and some where around 44 on the forearm. There should find about the same number of bacteria on each person and depending on where they swab the people.
ReplyDelete2. The study method is that there are samples taken from the patient and then are stored to look at later. Also that there are three stages of when the patient is getting looked at. The 1st is normal 2nd is a flare and the 3rd is two weeks after treatment. Also it is between inflammation allergies, and micro-biome skin cells. They then freeze it an make it to the point where they can look at it. Then they look for a specific gene an that gene is 16s. They found that if someone is causing inflammation by eczema it is by a skin barrier.
1. The relationship and number of bacteria to different parts of the skin is that bacteria causes the skin to react in different ways depending on what type of bacteria is affecting the skin. In the first article, Jake struggles with eczema and it does not stop itching so when he would scratch, it then bleeds, scabs, and gets itchier as well. The average human body is made of trillions of cells and houses about 10 times that number of bacterial cells. Many diseases are mainly indicated by interplay between many bacterial species.
ReplyDelete3. The role of metagenomic analysis is being used to study the skin microbiome where scientists compares thousands of genes present in the particular species’s DNA that they are working on. They make educated guesses based on the kinds of proteins that are made, what kinds of biological pathways that those proteins are involved in, and how different species may work with one another and with our own genome. Due to difficulty on sorting out which patterns are the start of disease against the part of normal variation between people, researchers may not have to decode the microbiome to better treat children’s skin diseases.
1. Describe the relationship/number of bacteria to different parts of the skin. Each organism that lives on our skin is localized to a certain part of our body. As the article said it is more likely to see the same organism on two different people's ears that to see it on different locations on one person's body. This could be caused because of the differences in nutrients available, salt concentration, ph of the location, temperature, moisture level, and many more reasons that could change living conditions.
ReplyDelete2. Describe the study methods that were used to study the link between allergies, inflammation, and the microbiome. The first method they mentioned was to use DNA sequencing to see what kind of microbes are involved, They did this by studying healthy people and recognizing which microbes are usually present on our body. They they studies people with allergies, inflammation, and other diseases to see what organism was showing in abnormal places or concentration. This way they can narrow their research and their therapy methods. By taking skin samples at different stages of the diseases, by taking swabs and media samples, they got enough DNA from the microbes. They ran PCR and amplified the genes or these organism and classified them by running the DNA fragments through DNA database. This is the future of disease diagnosis to figure out quickly what type of organisms are involve in the formation of disease and treat the patient for the specific microbe.