Here is the link to my Lab Report. Thanks for a wonderful semester! Wishing everyone a great summer!
Click here for lab report.
— Article and link: “Too Clean for Our Children’s Good? The Checkup’ by Perri Klass, MD, The New York Times, April 17, 2017.
— Summary: This article talks about the many various ways in which our children are protected from interaction with microbes, including giving birth by caesarian section, bottle-feeding, and possible exposure to antibiotics. Such protection on the one hand affords protection from disease but on the other hand offers greater risk that children may experience complications of the “built environment.’ It is a concern that living in such a clean, controlled environment could lead to an underdeveloped immune system and subsequent health problems which may have otherwise been avoidable had the body been exposed to a diverse array of microbes at a young age. In order to combat this problem, it is recommended that young children be introduced to these microbes in the outside environment through “controlled exposures’ in the form of either “natural exposure’ consisting of interaction with their environment or through a type of vaccine yet to be developed.
— Connections: This article include discussion of the development of the human microbiome, its importance in the overall health of an individual, the avenues by which children are typically first exposed to microbes, and also the concept of vaccination with microbes in order to improve health. All of these are topics which have been mentioned or discussed over the course of the semester.
— Critical analysis: I liked the contrast that the author provided between the microbes found outdoors as opposed to those found within the “built environment.’ While I had naturally assumed that the inside of a house or apartment may be “cleaner’ than the outside world, I had not given much thought to the members of the microbial populations to be found in each of the two environments; in reality, the inside of a dwelling is not necessarily any more microbe-free than the outside, it is instead simply inhabited by a different, and possibly narrower, variety of microbes. I did not detect anything scientifically inaccurate or confusing in this article, and think that it did perform an adequate job in relaying this information to the public. The author did not get too technical in any of their explanations, yet clearly stated the anticipated problem, reasons behind that belief, and also the possible solutions to the problem.
— Question: Are researchers suspecting that the health problems mentioned are primarily due to inadequate exposure to pathogenic bacteria? Or do interactions with the non-pathogenic bacteria also play a role in shaping the immune system of children? What kinds of “natural exposures’ are parents advised to pursue in order to assist their child’s immune system to develop properly?
Article: NASA Astronaut Kate Rubins Talks About Microbes
Date: August 3, 2016
Author: Kate Rubins, NASA.gov Video (youtube channle)
Summary: NASA Astronaut Kate Rubins talks about upcomming experiments on the Internatinal Space Station. These include understanding the microbiome of the human body and the microbiome of the spacestation itself. The astronauts can do this via protible DNA sequencers among other exciting new mirobial research equipment.
Connections: This vidio got me excited about the experiments being conducted on bord the ISS. They will be studying things related to subjects we’ve learned in class such as; microbial gene expression in microgravity, human immune system, bone and muscle system changes due to microgravity, understanding the human and spacestations microbiomes. They can do this with protable DNA and RNA sequencers. This is to connect the effects of spaceflight (microgravity, increased radiation, recycled atmosphere among others) back to the microbiome on Earth and other planets.
Critical analysis: I really enjoyed this vidio and it got me excited for the upcoming experiments the astronauts on the ISS will be conducting. I learned that DNA sequencing can be done with a device “as big as a cellphone”, which is very exciting for the future of microbiology. I also really enjoy NASAs vidios and articles, as I feel they do a great job expressing science so everyone can understand it.
Question: Would you want to go to the ISS knowing you’ll be potentially shairing microbiomes with your colleagues more rapidly then normal? This would be due to the tight quarters plus the recycled atmosphere and water systems.
Article: The Influence of the Microbiome on Allergic Sensitization to Food
Source: The Journal of Immunology
Within the last 50 years, there has been a major increase in the frequency of allergic diseases in developed countries such as the US. Genetics, combined with diet changes/improved sanitation/increased antibiotic and vaccination use, can be attributed with this change. These changes lead to a change in the makeup of the human microbiota, altering not only diversity but frequency as well. Specific species of bacteria can have a multitude of different effects on the body. The presence of certain gut microbes, such as E. coli, can help to stimulate a state known as “endotoxin tolerance,” which is thought to provide a protective effect against inflammatory responses. On a similar note, individuals with a lower risk of food allergies were found to have a higher prevalence of Bifidobacterium while those with a higher risk of food allergies was found to have a higher prevalence of Bacterioids. The makeup of your microbiota can have major impacts not only on your overall health but also on the way your body reacts to certain chemicals.
The article discusses the human microbiome and the effects of its’ diversity and makeup on health and inflammatory response.
I enjoyed the connections made between the human microbiota and human health/wellness. There is such a large connection between these, yet the field is so understudied it’s difficult to see its’ potential. One of the coolest thing I learned from this article is that when colonized with low-immunostimulatory microbiota in early life, aspects of immune education can be impaired resulting in predispostions to inflammatory diseases. This article is not a good read for those not strongly versed in scientific terminology, and is somewhat difficult for even bio students to fully comprehend due to terminology used.
How much of the field of preventative medicine is focused on the connection between the microbiota and human health? I’m curious about this because I feel like the field has so much potential, yet there doesn’t seem to be much emphasis on the microbiota and overall health.
Neanderthal Tooth Plaque Hints at Meals-and Kisses
Nature 08 March 2017
Summary: The plaque of teeth from Neanderthal remains discovered in El SidrÃ³n cave in northern Spain, which are estimated to have been from 50,000 years ago, were used to reconstruct the first microbiomes from extinct species. The researchers were able to determine their diet consisted of mushrooms and plants while Neanderthals from Spy cave ate wooly rhinoceros and mushrooms all from sequencing of the DNA from the plaque. The data also suggests that Penicillium mold was consumed along with aspirin from poplar trees to treat infections. The genetic analysis also suggests that Neanderthals and humans were kissing or sharing food as well since they both shared the same species of microbe in their mouths as modern humans. This is supported by the fact the strains did not split off until Neanderthals went extinct.
Connections: In lab we tested for some of the types of bacteria often found in the mouth using a variety of differential and selective agars. Though we were testing specifically for opportunistic pathogens, we discussed the amount of bacteria that is found in the mouth. In class we discussed the necessity and dangers of the bacteria that live in and on us and also the transfer of bacteria between people such as mother and baby. In addition, we learned about using penicillin as an antibiotic.
Critical Analysis: I found it very interesting that they could sequence DNA from such a long time ago. I thought the DNA would have degraded too much to get whole reads. It is amazing that they learned more about the social behavior of Neanderthals and humans just by the transfer of microbes. Since kissing means an intimacy during mating instead of the aggressive way they thought Neanderthals mated, the relationship between the two species is now considered different than what archaeologists previously thought.
Question: How did they track the split of the bacterial strain found in the ancient Neanderthals and humans from the same species of bacteria found in modern humans?
Article published April 3rd, 2017
Researchers from Birmingham University in the UK have developed an interesting alternative to using antibiotics for a certain rare lung disease that can be caused by several bacterium including P. aeruginosa. They would run a similar process to dialysis, called plasmapheresis, but instead of removing waste from the blood they would remove a certain antibody from the blood that was in excess, which prevented them from fighting the infecting bacterium. They would run this several times a week, replacing antibodies via blood transfusions, and this reduced hospitalization time and reduced the effects of it significantly, all without antibiotics. Research is being done to see if this is a viable replacement to some antibiotic treatments.
This relates to class material because we covered usage of antibiotics and how to prevent resistance. This would be a very good way to eliminate adding resistance to bacterium that can be fought this way significantly by not even using antibiotics.
I thought it was interesting how they are trying to find ways to avoid antibiotics completely, which would significantly decrease the worry of antibiotic resistance. It is a fairly new treatment, but it looks very plausible and accurate based on the reasoning in the article. It is fairly simplified for the public but is in depth enough so that the treatment process can be understood.
One question I would ask is how this could be expanded upon to more diseases beyond just filtering out antibodies from the blood. Could this be applied to other immune response diseases? People who are immune suppressed?
“Gut microbe mix may spark Parkinson’s’
Science News Magazine online article
December 1, 2016
This article describes several studies which, together, suggest that Parkinson’s disease is caused by the intestinal microbiome when it has a specific composition. It was found that the gut microbiome of diseased patients caused alpha-synuclein, the substance present in Parkinson’s patients, to clump in the brain compared to the gut microbiome of a healthy person transferred to mice with high levels of alpha-synuclein. In the second case, the mice did not show as many symptoms and the alpha-synuclein did not clump in the brain (this is what is believed to cause Parkinson’s disease).
We have discussed ideas of the human microbiome determining overall health. This has to do with the “ubiquity of microbes’, meaning they are found in all types of environments. We know that the bacteria in our gut produce byproducts while helping us break down and process our food. It is very interesting that they might be able to send signals to our brains. It seems like microbes must gain something beneficial by sending signals to the brain to make the organism act in a way that helps the microbe gain what it wants. We talked a little bit about microorganisms that infect insects to control them. The article was a summary of several peer-reviewed studies so I think they are credible. This is written in a very good way to communicate science to the general public since that is the purpose of this magazine. It pulls only the important parts of the methods and results to make it easy for the reader but also gives you enough information to critically think about it.
This topic makes me question many things like: What kind of chemical signals could microbes send to the brain to cause the symptoms of Parkinson’s disease? Is it a byproduct of their way of living or is it an intentionally released signal?
Title: A Microbe Hunter Plies her Trade in Space
Date: March 14, 2017
Summary: Microbiologist Kate Rubins has been investigating the unique microbiome of the International Space Station and establishing a microbiology lab in space. There has been 16 years of accumulation of the microbes brought by varying crews up from Earth, and microbes tend to stick around. While most of the microbes are harmless, some do have the potential to cause problems for crew, varying from infection to mold growing on the wall panels of the Space Station.
Microbiology in space is incredibly important to the future of space travel, be it for identifying alien life, preventing disease while in orbit, or simply improving the quality of life for spacefaring explorers.
Connections: We have been working to identify microbes from various environments and biomes, just as Rubins has, albeit from a less prestigious location. Being able to quickly and accurately identify microbes in all scenarios is something emphasized through the course, and Rubins is putting what we are learning to practical application whilst in orbit.
Critical Analysis: This article was actually a transcript of an NPR broadcast, and so read a little bit differently than most traditional news articles. It was filled with interview blurbs from Rubins, recollections of her time in space, and easy-to-follow explanations of her work. I know NPR works to tell stories as well as news, and this article was an interesting and engaging story. However, if you want the hard details about what Rubins was doing, or the specific microbial work done in the International Space Station, this is not the article for you. This is, more than anything, a story, and is not meant for conveying details. However, as a springboard for ideas, or an interesting illustration that your job can sometimes take you in strange and exciting directions, this is a good read or listen.
Questions: What other positions has NASA been searching for since it has stopped focusing on pilots? Rubins is a microbiologist, but what other branches of the sciences or other professions have gone to space?
Title: Even More Evidence Has Linked Parkinson’s Disease to Our Gut Bacteria
Source: Mark McRae from Science Alert
Date: March 4, 2017
Summary: Recent evidence has found that Parkinson’s disease may not only be influenced by the brain, but by gut bacteria too. Also, people’s bodies and the microorganisms they have may influence how they respond to the treatment provided to battle Parkinson’s disease. Even though studies are starting to make the link between microbes and Parkinson’s, these studies can help lead microbiologists and other scientists in the direction of making better medications and treatments for those fighting this disease.
Connections: There was a brief moment in the article that mentioned making medications specific to the individual that needs it based on the microbes within their system, which involved genetics. The bioinformatics lab gives us a glimpse into what goes into identifying bacteria based on their genetic sequence and the different functions that the bacteria’s genes carry out.
Critical Analysis: The title of the article caught my attention because I have been hearing more and more about Parkinson’s disease recently. Also, I was curious to see what the author had to say about other factors that play a role in this disease, instead of being just one component of the body. However, the way that the author wrote the article was a little confusing at times because it seemed as though the author would start to go into more details about the studies that they discuss, but then they would quickly become vague what the researchers were saying based on the results from the studies. Also, there were times that the author seemed to be a little disorganized when it came to presenting their thoughts and backing up their argument with a study.
Question: Since more studies are starting to link bacteria with the cause of Parkinson’s disease, is there a way to protect against these specific bacteria increasing the chances of someone getting Parkinson’s?