Hospital Microbiome

I read a Nature article discussing a project called the Hospital Microbiome Project. This projects entails researchers sampling all of the surfaces of a new hospital, such as the light switches, floor, and countertops, before the hospital became functional. The researchers then planned to sample and sequence the hospital when it became functional, although not only sampling the surfaces but also the patients that were living in individual rooms. This samples would allow the researchers to see what microbes were present on what surfaces at what times. The goal of this project was to see how microbes travel through the hospital. 

The article notes that after the hospital became functional, the research showed that there were significant differences between the microbiomes in different patient rooms. The study also showed that prolonged patient stay in a room, such as patients suffering from cancer, gave the microbes time to settle into the room, whereas the rooms of short-term patients returned to their previous pre-patient state more quickly. However the study also noted that a long-term patients microbe remained in their room after the room had been cleaned. 

While this study has not yet specifically found the transmission of any pathogens in the hospital in this way, I believe that it is something important to look at, especially as more and more is learned about the effects of the microbiome. If a patient is treated with an antibiotic, will they be colonized by the microbiome that the previous inhabitant of the room left behind? The implications of this could be potentially large, especially if we find that the microbiome can contribute to diseases or have effects on weight or personality. It would be interesting to see how long it takes for a new patient’s microbiome to replace the microbiome of the previous patient. This may also have implications for shared patient rooms, and how one patient’s microbiome affects the other patient. More research needs to be done on this topic to not only determine these issues with the “normal” microbiota, but also when potential pathogens may be brought in to the hospital by one patient and could potentially be transmitted to others. 

The link to the nature article is here:

And here is the link to the Hospital Microbiome Project webpage:


Probiotics to treat MRSA

An interesting study from February of 2013 discusses the possibility of using probiotics to treat MRSA (methicillin-resistant Staphylococcus aureus). This probiotic would use the fermentation of glycerol by Propionibacterium acnes in order to treat MRSA as a bacterial interference therapy. The paper defines bacterial interference as the use of commensal bacteria to prevent colonization of pathogenic microbes. P. acnes is a normal skin resident microbe that is the paper notes is hosted by everyone, is known to be able to ferment carbohydrates to propionic acid, which has antimicrobial properties. In fact, some of the results of this paper suggest that propionic acid could potentially have broad anti- S. aureus activity, while potentially not harmfully disrupting the normal skin microbiome. The paper notes that the body exploits the fermentation of P. acnes in deep, anaerobic abscesses to prevent the entry of S. aureus into the bloodstream, reducing the risk of S. aureus infections.This means that it is possible that this process exists as a natural part of the microbiome that exists on our skin. 

I believe that it is possible that this study and perhaps more that may validate or strengthen these findings could have huge implications for the treatment of infections and potentially diseases. This treatment in particular would be especially useful because MRSA is resistant to common antibiotics. However, if more sources of naturally occurring treatment could be found, it is perhaps possible that we could get rid of or at least lower unnecessary uses of antibiotics, in turn hopefully reducing the risk of antibiotic resistance. If more treatments like this are found, they could be used to treat other bacterial ailments without having a negative, disruptive effect on the microbiome. More research should be done on these type of treatments in order to determine when they are possible and how effective they could be. 

Here is the link to the study:

Is it our duty to participate?

A subject that we have danced around some during many class discussions is the topic of whose duty it is to participate. Who is responsible for providing subjects or samples for scientists to study? People can be useful to research in many ways, from donating their time and allowing themselves to be screened such as in an MRI to donating their samples to a biobank in order for researchers to use these samples in current and future projects. The question of whose responsibility it is not only comes up in our class discussions but also in the book that we are reading. No one can seem to give a clear, or at least agreeable, answer as to who it should be. I say that no one can give an agreeable answer because no matter what is said, it seems as though it can be argued. We seem to have a lot of mixed ideas about whether or not we should feel a duty to participate in research. However, I have a tendency to side with the authors in the book. I believe that there should be some kind of duty to participate in scientific studies of some sort. While we may not have to participate in all of them, I believe that it is important for individuals to make an effort to help to further the research that is being done. Why? Because it is likely that we can all benefit from the advances that are being made from a lot of the research that is being done. If people sign up for studies that can contribute to finding a cure for cancer or some other widespread disease, it is also likely that we will all benefit from these research outcomes, at least indirectly. While we may not each develop cancer, or whatever the disease may be, it is likely that our family members or somebody else dear to us will be diagnosed with a disease that has the potential to be treated by current research. So to me it seems that everyone is likely to receive a benefit if we continue to increase our knowledge. This is why I believe that it is important for people to make an effort to participate. To me it seems that we can compare this to a group project. If everyone participates and gets a good grade there are no problems. However, if only half of the group participates and manage to get a good grade, the other half of the group just gets a free ride and also receives the benefits. To me this seems unfair. While I understand that not all people are comfortable with participating in research and this is fine, I do believe that it is important for those of us who are willing and able to take part. 

Now, all this being said, I have never participated in research. I quite frankly have no idea how to get involved. And this is where I believe that the people doing the research need to step up their game. I believe that information on how to become involved by participating in studies needs to become more readily available. I believe that more people would participate if they easily had access to the information that informed them on how to do so. Instead, it seems as though people have to search out on their own how to get involved, and this may be part of what prevents people from getting involved. In order for scientific knowledge to continue to advance, I believe that it is important for both the public to change their view on the importance of getting involved and also for the researchers to make their recruiting tactics more openly available to the general public. 

Pharmaceutical companies getting involved

I found an article on the Med City News website that discusses that Pfizer has just enlisted Second Genome, a microbiome company, to perform a study exploring the role of microbes in disease, particularly obesity. Second Genome, “The Microbiome Company”, describe themselves as bringing “microbiome science to the discovery and development of therapeutic products”. This study will look at the relationship between the microbiome, obesity, and metabolic disease by studying 900 obese individuals over a twelve month period.

While we have discussed in class the importance of looking into new therapies utilizing the microbiome, I wonder if studies funded by a big name drug company are really the way to go about this. While Pfizer likely has the money to fund a project like this, it is easy to wonder whether or not their intentions are sound. If the study is performed well and the evidence is found to be strong and could help people, than I believe that it is worth while. However, if the study is performed in a way in which the company looks at only the results they want to see, or perhaps if the potential therapies are not studies to their fullest extent, than it could end up being detrimental to people. In other words, if Pfizer is funding this study in order to advance knowledge and help people, I believe it could be useful but if Pfizer is dishonest and uses this project and potential therapeutics only to make money without helping others, than I believe it could be a huge detriment to people who are looking for real solutions. We discussed in class the other day that intentions behind a study can determine whether or not it is performed ethically, and that a conflict of interest can potentially stand in the way of a study or trial being done well. If Pfizer has a potential to make a lot of money from this project, there is also potential that they will cut corners when it comes to doing the research correctly.

The link to the article about Pfizer joining up with Second Genome can be found here:

If you’re interested in learning more about Second Genome, their webpage can be found here:

Hunter-gatherer microbiome

An article that I looked at on the National Geographic website looked specifically at research being done on the Hadza tribe in Tanzania, a group made up of hunter-gatherers.  Because this tribe does not grow crops or keep animals, the article discusses that this study allows us to look at this group of people as the closest approximation of what ancestral gut microbiomes may have looked like 10,000 years ago, or before agriculture came around. However, the article is careful to point out that the information received from this tribe is not exactly the same as the ancestral gut, as these people are modern people that likely have access to things that our ancestors didn’t. Along with this, the article notes that, perhaps as expected, the microbiota of the hunter-gatherers were more diverse than the microbiota samples taken from a group of Italians at the same time.

Along with pointing out different portions of this study, I believe that this article also does a good job of bringing up two different points. The first of these points is that the microbiome project as a whole is in need of expanding the research that is being done. It notes that while some small studies are being done on non-Western civilizations (Burkina Faso, Venezuela, Bangladesh, Malawi, and this study in Tanzania), most of the research includes Western, industrialized nations. This lack of diverse research may cause skewing of what our idea of what the microbiome entails. I believe that it is important to consider many different lifestyles when researching the microbiome in order to see the most complete picture of what is going on.

Another interesting thing that this article is sure to point out is that the Hadza microbiome is not necessarily better or worse than our Western microbiomes, but is perhaps just better adapted to the lifestyle that they are living. For example, the article points out that the Hadza guts do not have Bifidobacteria, a bacteria that seems to make up about 10 percent of a Western gut. However, the Hadza gut does seem to contain some members of the Treponema group, certain species of which can cause diseases such as syphilis. As one researcher points out, the presence of this group may be a warning sign for a person in the Western world, but does not seem to cause any issues within this group of people. I believe that these differences go to show how much diversity exists in gut microbiomes across the globe, and why it is important to include samples from groups with many different backgrounds in order to create the best picture of what the microbiome is all about.

Here’s the link to the article:


The Healthiest Microbiome

While looking around the internet for something to write about, I came across the blog of Jeff Leach, the founder of the Human Food Project. In his blog, he discusses what will be his year-long journey to “the healthiest gut microbiome in the world”. He discusses how he will be altering his diet in many ways over a year and keeping fecal samples throughout in order to figure out how different aspects of his diet will affect his gut microbiome.  

There are two things that reading this blog about his plan for his journey caused me to think about. The first of these is the possibility that a person’s diet may underly a lot of the differences that we see in the microbiome. In class and in some blogs it has been discussed all of the things that can cause differences in the microbiome: culture, ethnicity, location, and education level, just to name a few. However, is it possible that the underlying cause of some of these differences could be the different diets associated with these factors? Each of these factors may cause a person to have a distinct diet, and these dietary differences could contribute to the differences of these groups that are seen in the microbiome. While I am sure that diet is not the only cause of these differences, as two people with identical diets probably would not have identical microbiomes, it may be a greater factor than we thought. 

The second thing that this blog made me think about was the idea of “the healthiest gut microbiome”. I know that this is a concept we have talked about some in class, but is there really a healthiest microbiome? It seems to me that if everyone’s microbiome is unique, how can we truly classify one microbiome as the healthiest? This is especially complicated because there are many different kinds of healthy people with different lifestyles that likely have different microbiomes. How do we classify what is healthy and what is not? The fact that some bacteria are harmful in some people and not harmful in others seems to complicate this issue. Perhaps it would be easier to classify what microbes (or combinations of microbes) are only detrimental in the gut, as opposed to finding which balance is best. 

The blog post from Jeff Leach can be found here:

Issues with Research Funding

I found the discussion that we had in class on Tuesday about research funding to be rather interesting and a little frustrating. I found an article from 2011 on Scientific American discussing “The Broken Science Funding System”. This article points to a 2007 study that showed that U.S. university faculty members spent about 40 percent the time they had for research “navigating the bureaucratic labyrinth”, which I understood to mean applying for grants, although I suppose it may also include some other activities such as reviewing other articles or trying to get published. It also points out that the National Science Foundation found that between 1997 and 2006, an average applicant had to submit 30 percent more proposals in order to earn the same number of awards. This seems like a very large increase in the amount of time and effort that must be dedicated to being funded over a ten year period, and I wonder how much it has changed in the eight years since. 

To quote the article, this funding system “not only…makes inefficient use of scientists’ time, it discourages precisely the kind of research that can most advance our knowledge”. I could not agree with this point more. One example of this is what Dr. Duffin pointed out in class the other day: the old, well-known professor is much more likely to receive funding than their younger, less-connected counterpart. This to me seems like an entirely skewed system. For one, it seems to me like this may discourage young people from wanting to be researchers, as it seems so difficult to be funded and be able to pursue their ideas. Also, this seems to be an issue because it may prevent people from doing truly risky and innovative research. If funding only goes towards “safe” projects (whatever safe means), why would researchers feel challenged to try something out of the box? While I understand that the people giving grants do not want their money to be wasted, to me it seems that any new research in which the experiment is conducted well and it produces results can be useful in teaching us something. If researchers are not encouraged to challenge themselves by doing something that seems a little bit risky, how are we supposed to learn? I believe that there has to be some way to change the funding system so that it encourages researchers’ curiosities instead of shutting them down. 


Here is the link to the Scientific American article: