Author: Narmada Dhakal

• Can experiments detect differences that matter?

I think that it is important to remember that while experiments can detect similarities and differences, it is true that not all of them matter. I think that when interpreting literature we need to look out for gaps in our understanding. We definitely do not have all the tools right now to look at differences without knowing exactly what it is that we are looking for

• Does the study show causation or correlation?

Whenever we are looking at a study it is important to determine the claims they end up making about their study. We need to be able to determine if what is being reported is causal or just correlation. I think it is really easy to assign causal relationships without that actually being true.

• What is the mechanism?

When 2 factors are correlated then there is some sort of relationship those two variables we are examining. This all comes down to mechanism. After something is determined to be related to something else, then we need to determine how those two things may be related.

• How much do experiments reflect reality?

They honestly do not. I think that in addition to microbiomes, when we are looking at the human body or any other biological systems, we need to understand that they are much more flexible than our experimentation system. There is no way experiments perfectly mimic reality, but they do represent aspects of reality.

• Could anything else explain the results?

This is an important question to ask in every study done. There are many confounding variables that could be presented and not discussed. It is extremely important to look at the results and not abandon specificity.

I think that reading about the first free-living organism to have the entire genome sequenced is pretty illuminating. I appreciated the fact that I pretty much understood their process of work (except for the complex math things in the beginning). I think that at this point it is easy to imagine sequencing the genome of a bacteria because we consider them to be relatively small and not as difficult. To see where science has gotten is very fascinating. I think the genomic sequencing of this organism opened up a wider path. The commentary was very helpful in guiding readers to how far genomic sequencing has progressed due to the work Haemophilus influenzae. After this genome was sequenced, John’s Hopkins made a collaborative effort to sequence 30 more microbial genomes.

Adèle Mennerat and Ben C. Seheldon, in their paper entitles “How to Deal with PCR Contamination in Molecular Microbial Ecology,” assert that enzymatic treatment of PCR reagents help reduce contamination. The authors provide evidence that two enzymes, DNase 1 and SauAI both reduce contamination but DNase also shows substantial reduction in bacterial richness while SauAI does not affect richness and simultaneously reduces contamination. The purpose of this paper is to encourage use of decontaminating reagents in order to start setting this as standard procedure. The authors establishes a scholarly relationship with academic in microbial ecology as well as other biological sciences.

Mennerat, A., Sheldon, B.C. How to Deal with PCR Contamination in Molecular Microbial Ecology. Microb Ecol 68, 834–841 (2014).

To be perfectly honest, the chimera exercise was extremely difficult for me. I had a really hard time understanding the directions just because this is not something that I had ever done before. The commands were difficult to understand, and trying to remember the different commands that we had used throughout the previous exercise was also something that was difficult. Something that would have helped me was having a video of one of the instructors going through the commands and explaining it so that I could have another way of learning and understanding – since with online classes its a little more difficult to ask questions. However, while it was not an easy feat, I think that I did end up understanding everything by the end of it. In fact, I developed really great appreciation for the Usearch program. I had used BLAST in the past, however, I truly understood the benefits of the Usearch program. I think that with a little bit of practice with the commands, I can definitely use this in the near future. Additionally, I think the chimera exercise also brought my awareness to what chimeras are and why they are important. I did not even think about this concept before this class so I am really happy to have learned about chimeras and how to identify them in nucleotide sequences.

During the most recent panel review I saw a lot of really fantastic proposals. Most of the proposals were really thought out and clear and obviously had a lot of work put into it. One thing I realized was that the panel review process is very meticulous. My group and I reviewed every sentence of every proposal. We wanted to make sure that it met all of the criteria and constantly discussed how it would impact the respective fields. I think this influenced me the most because while we were pretty tough in analyzing everyone’s paper, the process of reading about all of these different topics was so fun! I think that doing research can be extremely draining but seeing the amount of effort and care that students put into their proposal was really inspiring. It makes me want to work much harder. I was also amazed by the amount of detail that some students put into their paper. While my paper was detailed, I think I may have missed a few key aspects of my proposal that would have definitely made it better. My experimentation process was solid but I did not have enough information in my intro about the potential health impacts of my topic. In the past, I have also noticed that my intro for proposals are somewhat lacking so I will definitely take this common mistake and try to remedy it in the future. When it comes to experimental design, I am pretty confident in my abilities. Quantifying microbes and sampling are some of my strengths and I am equipped to make experimental designs around these aspects of research. I think that something I could always improve upon is making sure that I cover all confounding variables that could possibly occur in the experimenting process.

Kelley Scott and Jack Gilbert in their paper entitled “Studying the Microbiology of the Indoor Environment” assert that humans spending a lot of time in the built environment (indoors), away from fresh air, might increase rates of chronic and acute illnesses. Gilbert and Scott provide evidence that bacterial 16S rRNA sequence diversity from over 200 samples from pools, bathrooms, showers, toilets, and other commonly used surfaces around different houses, all contained bacterial pathogens. The purpose of this study is to examine the ecological interactions between microorganisms built environments, as well as study and identify pathogenicity. Gilbert and Scott establish a scholarly relationships with academics in specifically bacterial molecular genetics and ecological genetics.

Peer review is the process of subjecting research to close examination by others in the same field. This can determine if a study should be published, reviewed or even completely rejected. However, even this process has numerous flaws. First of all, the peer review process is extremely prone to bias. Women are greatly underrepresented in the peer review process – this does not help with the already rampant problem of sexism in science. Specifically, there is evidence that women do not receive as many grants as men do during the peer review process. This blatant sexism I obviously problematic, however, there are definitely different solutions to make this process fair. There are many options to improve the peer review process. Blinding the reviewers, training them, opening up the process to the world or selecting the reviewers carefully, are all ways to try an improve this process. Hopefully changes happen soon but until then, the peer review process is the best we have for research criticism and examination.

I actually had a really good time with the peer reviews. It was a little difficult compared in-person peer reviews because I felt like it would have been easier to comment on things right on the paper. It felt a little tedious to go back and forth between 2 tabs constantly to write about things that I wanted to compliment or critique. Besides that technical aspect of the peer reviews, I think that something I really enjoyed was looking at other people’s citations. Personally, I did not have enough time to complete my citations because I think that I was confused as to what style I needed to use…but now I am thinking that I should have probably used ASM. I noticed that the papers I reviewed wrote about their procedures in a really concise way – it wasn’t too long and it was also super clear. I think this is definitely something that I will be fixing on my paper. Something else I noticed was that a lot of people were a little repetitive in their introduction which is also something that I believe that I did on my paper. I will also be correcting this on my paper. I am looking forward to seeing how other people corrected or critiqued my methods/procedures. While I was writing my paper I was wondering if there was a more efficient way for me to conduct my experiments. I am hoping that people gave me a couple of ideas.

A microbial population can be identified based on many characteristics, such as: morphology, cell arrangement, reproduction, growth, metabolism, pathogenesis and genetic properties. There may be many approaches to classifying and organizing a microbial population. On the other hand, a microbial community is defined as a group of microorganisms that live in the same space. This is not limited to the same types of microorganisms. In other words, in a microbial community the populations of that community may interact in may ways, for example, as predators, preys, or they may even be in symbiosis. A microbial community can be seen as smaller than a microbial population. Due to this specific distinction, microbial populations are more easily manipulated for research purposes.

Citations:

https://www.britannica.com/science/microbiology

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