Third Microbes in the News

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— Article and link: A Blazing Hot Coal Shows How Microbes Can Spring to Life   Source: Wired 04/21/19   Link: https://www.wired.com/story/a-blazing-hot-coal-seam-shows-how-microbes-can-spring-to-life/

— Summary: In Centralia many single-celled microbes live in the soil that is on top of the underground mine fire in the coal seam. Due to the fire it was initially thought nothing may have lived, but instead there are many microbes. The same amount of microbes have been found to be living in very hot areas including various thermophiles that microbes that live at geothermal hot springs.

— Connections: In class we have briefly studied thermophiles which are heat loving bacteria. We have also looked at the various species of microbes that live in soil, and I find it interesting how natural disasters can affect what microbes are in the soil. We studied factors that can cause microbes to go dormant, which is what can happen during a fire since there is no activity on the soil.

— Critical analysis: I thought this article was interesting because it involves microbe activity when a natural disaster occurs and using spores to regrow genomes. The article was well written and contained a large amount of detailed scientific information. It could be rather difficult for the general public to read the article and understand it all though, because of all the technical terms it contains.

— Question: What organisms do you think would be likely to live through a fire or other extreme natural disaster? Would they become dormant?

 

 

A2: Microbes in the News

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Title: Microbes that live in fishes slimy mucus coating could lead chemists to antibiotic drugs

Source: The Conversation Academic Rigor, journalistic flair

Date: March 31st 2019

https://theconversation.com/microbes-that-live-in-fishes-slimy-mucus-coating-could-lead-chemists-to-new-antibiotic-drugs-114278

Finding new sources of antibiotics has become critically important in recent years in order to combat drug resistant infections. One potential source is fish mucus that covers their bodies in pill form since it is a natural anti-infective. Over 33,000 species of fish have the microbial containing the slime that can protect them from diseases and bacteria and potentially used to help humans with this as well.

In class we have discussed antibiotic sources and working around antibiotic resistance. We have looked at how different natural microbes can help with fighting off diseases and not have a resistance already built up.

I found the article to be well written and very scientifically relevant. They referenced their research at Oregon State University and the ways they have classified the different bacteria they have found taxonomic groups. They found 47 different bacterial strains gathered for the swabs they did on the fish mucus. They carried out a process similar to what we have done in lab to isolate and test them.

What do you think about using natural anti-infectives from animals to combat human pathogens?

A2: Microbes in the News (#2)

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Bacteria in probiotics can evolve in your gut and turn nasty, study shows  (The Independent)

Link: https://www.independent.co.uk/news/health/probiotic-bacteria-gut-health-ibs-bowels-a8840636.html

Summary:  This article talks about a study performed at the University of Washington in Missouri where a probiotic evolved to attack the protective coating of the intestine in the mice they tested. Unhealthy mice with low gut microbial diversity were more likely to develop an evolved strain of the  E. coli Nissle bacteria that was used in the probiotic they studied. According to the researchers, their findings have implications for the development of safer probiotics in the future.

Connections: This article is very relevant to the human microbiome section that we covered in class. It involves the gut microbiome and the ways it can be more or less healthy, and more or less diverse. I think the way microbes can change and evolve right under our noses is fascinating!

Critical analysis: This was certainly an interesting piece and the writing style flowed well. However, this study is only one of many and might mislead readers to think that all probiotics can “turn bad.’ It could also be confusing to the regular reader, because the wording of the article makes it seem like probiotics are drugs that can change inside your body. Of course we all know that probiotics are made up of living bacterial cells that are supposed to help enhance the diversity of your gut microbiome. It was also unclear whether the  E. coli strain always evolved in a negative direction or if it was simply more prone to evolve in an unhealthy gut microbiome (toward good or bad characteristics, we don’t know). Overall, this was a well-written article, but I think the writer conveyed what he wanted the readers to believe and not necessarily the actual truth of the study.

Question:  What were the exact parameters of the evolution of  E. coli Nissle observed in this study?

New technique provides a better understanding of bacteria evolution

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New technique pinpoints milestones in the evolution of bacteria
Results show bacterial genomes provide “shadow history’ of animal evolution.
Jennifer Chu, MIT News Office February 7, 2019

References

Danielle S. Gruen, J. M. (2019, January). Paleozoic diversification of terrestrial chitin-degrading bacterial lineages. BMC Evolutionary Biology, 19-34. Retrieved from https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-019-1357-8

 

—  Summary:  Researchers from MIT have established organism relationships between fungi and bacteria by reviewing the gene for chitinase (an enzyme which helps to break down chitin). Their review of the mutations, and similarities across different species has allowed them to create an evolutionary tree which correlates microbial evolution with fungal evolution. They found that approximately 450 to 350 million years ago, diversification of three separate bacterial groups diversified as the result of gene transfer with a chitinase utilizing fungi. Below is the resulting evolutionary tree with the fungi identified by purple lines and bacteria with blue lines.

(Gruen, et al. 2019)

—  Connections:  This connects with: Microbial evolution, metabolism, and diversification.
Chitinase allows these bacteria to metabolize chitin as an energy source. This allowed diversification of microbes into new niches ones chitin became more prolific in the environment. Gene transfer was said to make it difficult to genomically identify or differentiate bacterial strains, but here the gene transfer has allowed a better understanding.

—  Critical analysis: I found this article very interesting because, most evolutionary trees are based on rRNA sequencing (highly conserved due to form/function). The use of chitinase to correlate evolutionary relationships between fungus and bacteria is interesting. Especially since the origin of chitinase was in a Fungi (a microorganism that doesn’t look like a microorganism) and the gene has been horizontally transferred to bacteria.

The story was very well written and after reading the original journal publication, it was factually and accurately written. The author did as great job in conveying the information to the general population without losing the integrity of the research. I appreciate the writing style and how it helps those (like myself) who aren’t as well versed in the scientific nomenclature, to understand the information and findings from the research.

 

—  Question:  How many other highly conserved coding regions can we isolate and use in this manner? Are enzymes such as chitinase always highly conserved, or is there slight variations in the conformation, allowing it to mutate without ruining the function of the enzyme?

-Samantha Smith

A2: Microbes in the News – New Anti-CRISPR Proteins in Soil Bacteria

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Article and Link: New anti-CRISPR proteins discovered in soil and human gut (ScienceDaily)  https://www.sciencedaily.com/releases/2019/02/190205144338.htm

Summary: CRISPR is a natural bacterial immune defence, but some bacteriophages (or viruses) have developed anti-CRISPR genes that cause bacteria to lose immune defence when infected. New anti-CRISPR proteins were discovered by using protein functionality tested across a variety of environments, rather than using DNA and culturing. Their discovery could lead to the development of better technologies in the emerging field of CRISPR gene editing.

Connections: This article demonstrates the prevalence and possible uses for bacteria in today’s medical world. If bacteria could be used to produce proteins that create more precise gene editing with CRISPR, gene editing may have a very real future in human society. The way the researchers discovered new anti-CRISPR proteins is also a testament to the diversity of microbial life and how not all microbes can be cultured.

Critical analysis:  I find this article fascinating, because I am very interested in how cellular function, protein production and genetics can be used in the medical world to produce new treatments, drugs and cures for disease. With improved CRISPR technology, it may be more realistic to use gene editing to treat diseases such as cystic fibrosis. Unfortunately, this article was not very well written and did not explain the methods of the researchers in a way that is accessible to the public. The writing was very hard to follow and I had to read it multiple times before I began to understand the premise of the article. However, from my level of understanding there were no factual inaccuracies even though it oversimplified genetic editing and the way CRISPR works.

Question: How does the presence of anti-CRISPR genes in bacteria affect their susceptibility to antibiotics? Could they be more susceptible since anti-CRISPR proteins target bacteria’s “immune systems’?

Microbes in the News

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Title: For zombie microbes, deep-sea buffet is just out of reach

Date: January 22, 2019

Website: ScienceDaily

Source: Woods Hole Oceanographic Institution

Link to Article:  https://www.sciencedaily.com/releases/2019/01/190122104617.htm

Summary: This article discusses microbes below the ocean floor that posses some odd characteristics, such as slow-motion growth. The Woods Hole Oceanographic Institution performed some research on these curious microbes and found that the organisms are not fully utilizing molecules available in their environment. Although the microbes should be able to take advantage of the carbon in the sediment, as it is in a form that they are able to metabolize, they fail to do so. One researcher concluded that the microbes can not access the molecules because they are physically too far away. Moreover, the microbes don’t have sufficient energy to acquire the sporadically located molecules. This research could potentially aid in obtaining further knowledge on not only microbes, but other organisms as well.

Connections: As we have been discussing in both lecture and lab, microbes need specific conditions to survive and reproduce. For example, various agar plates, with differing quantities of ingredients and nutrients, are used to cultivate microbes. The research in this article demonstrates the vast deviance that microbes have from one another. While some need constant access to high levels of nutrients, others, like the ones discussed in the article, can survive by other means. It is vital to be aware of and comprehend these differences when working with microbes both in and out of the lab.

Critical analysis: This article initially caught my eye because of the bizarre title, and I was further intrigued to learn about these microbe’s survival. I was aware that microbes inhabit a prodigious range of environments, however, this article opened my eyes to just how much microbes utilize various resources. Furthermore, I usually associate microbes with rapid reproduction, however, this research reveals that it can take years for cell division to occur. Overall, the article and the research backing it seem scientifically sound. However, from my perspective, this article was slightly misleading, and therefore failed to accurately communicate science to the public. Although I recognize the use of the term “zombie microbes’ in regard to the article, I was expecting different content within the text. I think individuals may incorrectly attribute features to the microbes based on phrases used in reference to the microbes “zombie-like’ characteristics.

Question: The article mentions that the microbial geochemist, Colleen Hansel, asserts “this research may help us understand some of the limitations on life in general’. What applications might this research have in helping us gain information about the world around us (i.e. give an example)?

A2: Microbes in the News Assignment

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Microbes in the News !

Over the course of the semester, post 3 different stories involving microbes  from the popular media and then read and comment on 3  posts by other students.

 

Points: Total possible = 30 points. Earn up to 8 pts for making a post and 2 points for posting a comment. Create 3 posts and 3 comments over the course of the semester.

Deadlines: Posts can be made as soon as you’d like, but for full credit you must post them by these deadlines:

Post 1: Feb. 8

Post 2: April 1

Post 3: April 15

All comments: April 15

 

Learning Objectives:

– Increase your awareness of microbiology and its role in society

– Expand and apply your knowledge of microbiology

– Practice critical thinking by analyzing popular news media for scientific accuracy

– Develop questions about microbiology

– Help your peers and yourself understand microbiology by answering their questions

 

Instructions:

Over the course of the semester, create 3 separate Microbes in the News posts on the course website, and then read and comment on 3 Microbes in the News posts by other students. Be sure to follow the guidelines below in order to qualify for  full credit.

 

Guidelines for creating a post:

– Article and link: Enter the title, source, and date of the article and create a link to it. Articles should be from any popular media source (newspaper, magazine, podcast, blog,  etc.) that others can access without hitting a paywall. Any relevant story is acceptable, but challenge yourself to find stories that are current (~within the last 3 months) and that haven’t yet been posted by your peers, whenever possible.

– Summary: Write a short summary of the story (just a few sentences is sufficient).

– Connections: Explain briefly how this connects to what we’ve covered in class.

– Critical analysis: Explain what you found interesting about this story, and what (if anything) you learned. Comment on whether you think the story was scientifically accurate or not. If you noticed any factual inaccuracies or aspects of the story that might inadvertently confuse or misinform readers, identify those and provide a more accurate explanation. Also comment on how this was written. Do you think it did a good job of communicating science to the public? Why or why not?

– Question: Write a question about microbiology that you had as a result of reading this story.

– Categorize: Categorize your post as “A2: Microbes in the News’ using the categories menu on the right. This will ensure I can find it and give you credit.

– Tag: Tag your post based on any relevant microbiological themes by choosing from the tag menu (below categories on the right). Use existing tags when possible, but you can add new ones if needed by clicking “+Add New Category’ link just below the list of tags. This will help us find stories on relevant themes. You can also use these tags to search for other students’ stories on themes that interest you.

Guidelines for commenting on a post:

– Read the news story and the students’ post about it

– Create a comment and write a response to their critical analysis. Do you agree, disagree, or have more to add?

– In your comment, answer their question to the best of your ability. This might require some independent research.