A2: Microbes in the News – Scientists Discover Nearly 200,000 Kinds of Ocean Viruses




Researchers have assembled data from a global sampling expedition using genomic analysis and have increased the number of known oceanic viruses twelvefold.


This is a story of people using the tools which we have been using to study the viruses we have been studying and improve the body of knowledge we have in this field.

Critical Analysis:

While microbiology has been studied in some manner since the early days of science the changes in the accuracy or our tools and the price of using them can dramatically change what we are able to accomplish. This article is just one example of how much more there is to learn in this field.


With a single study able to make such a large impact on the amount known, the question becomes how much more is there to know? I would not be at all surprised to see another twelvefold increase with the next study and another after that. If there is one thing that I have learned from this class it is that the microscopic world holds a multitude of secrets yet to be discovered.

Civilization is Born – Matt Andrews


“Civilization is Born” by Matt Andrews

Artists Statement:

A virus is in some respects a pure expression of information made manifest. It is like a book, it exists and anything that happens because of what it contains is dependent on the life which reads it.

The only difference between humanity now and humanity a hundred thousand years ago is the information, be it science, culture, or other knowledge which we have accumulated and spread among ourselves.

In this piece I have drawn inspiration from viruses, to that end I havbe created a scene in a 3D program where I modeled the delivery protein structure of a virus bacteriophage including the icosohedral head, tail, base plate, and tail fibers, all of which I have scaled up to a size closer to that of a human, the DNA has been replaced with a book.


Some larger renders of this scene:

Civilization is Born

Art Project

The diversity of the microbial world is not only astounding, but awe inspiring. Life as we know it would not be possible without this vast microbial community and oxygenating our atmosphere, cycling our nitrogen, and fixing our carbon. These and so many other processes, allow us to inhabit this Earth and continue to thrive. However, there is still the <1% of microbes which are classified as pathogenic to humans. These microbes, do not help our quality of life but rather, can cause disease and death in our populations.


Since 2015 the World Health Organization (W.H.O.) publishes a yearly list of pathogens. These pathogens are those which have been identified to pose the greatest public health risk due to their “epidemic potential and for which there are no, or insufficient, countermeasures.’ (World Health Organization, 2018). The pathogens which are the subjects of my portrait collage are those of the 2018 R&D Blueprint List of priority pathogens. (https://www.who.int/blueprint/priority-diseases/en/)

For my art project I have done small portraits of the pathogens listed by the W.H.O.. It should be noted that these are in no particular order. All of these pathogens are in need of further analysis as well as analysis for treatment methods which would be imperative for stalling an outbreak. One should also note that there is a “Disease X’ within this collage. There is no true disease called Disease X, but rather the potential that an as of yet unknown pathogen that could cause widespread disease epidemics is out there. It is my hope that even though my artistic abilities and nudges to 70’s rock bands may not be the best, they can introduce this information to a broader audience. Since not everyone spends their free time looking at the W.H.O. website.

-Samantha Smith

A2: Microbes in the News 3

Cold Plasma can Kill 99.9% of Airborne Viruses

Science Daily

April 8, 2019


Summary: Non-thermal plasma such as sparks from electrical discharges has proved highly effective in killing viruses in the air in just seconds. This is achieved by forcing air through a space in which electric sparks are being made.

Connections: From the classroom we have learned how viruses in many ways are a unique “lifeform” requiring sometimes unique solutions to deal with.

Critical analysis: This article is fascinating from a medical technologies standpoint. Air transmission of viruses had always been a concern as it is uniquely difficult to stop. This has a variety of potential applications, but the primary area of interest is hospitals.

Question: Do you think that this can be practically implemented in hospitals and other medical facilities.

A2: Microbes in the News

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


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 (Post 2)

Title:  Are viruses the best weapon for fighting superbugs?

Source:  The Conversation

Date Published:  March 6, 2019

Link: https://theconversation.com/are-viruses-the-best-weapon-for-fighting-superbugs-111908

Summary:  This article was written by a physician who is a specialist in infectious disease, he was interested in reviving an alternative to antibiotics called phage therapy (using viruses!). Which is using phages to kill certain harmful bacteria as an alternative to antibiotics that can wipe out good bacteria with the bad.He does point out this technique was tried in the 1920/30’s and had pros and cons but ultimately lost to antibiotics because it was harder to maintain with the limited knowledge of the day. However, now that we know a lot more about phages they can be more effectively utilized to target bacteria as an alternative to antibiotics. This can potentially help prevent ‘superbugs’ or bacteria that is highly antibiotic resistant, and ween America from its extremely high antibiotic dependance.

Connections: We have recently been covering viruses in class and learning about how they operate to infect bacteria which directly relates to this article.

Critical analysis:  I found this article interesting because it helps highlight how phages (or viruses) can be really useful moving forward. The word virus is almost always used with a negative connotation but it is important to realize it can be helpful. I believe the article holds a semblance of accuracy because the author is in fact someone who is a specialist in infectious disease, and highlights the pros with the cons providing an argument from all sides which is important. Also it is simple enough in the jargon that it can be an article shown to the general public and still convey its general message, and stir interest in phage use for medical treatment which I think is the overall goal of an article such as this.

Question:  Do you think people would ever be able to accept using a phage to kill bacteria in their body? Would you be able to?



A2: Rubella cases exceed 100 in single week

NHK World, 3/5/2019


Japanese health officials have reported 109 cases of rubella in the week of February 18-24th. This brings the total 2019 rubella cases in the country to 650, four times higher than the same period last year. Officials predict that this year may be comparable to 2013’s record year of over 14,000 cases. The national government has begun offering free vaccinations to males between 39 and 56, an age group that did not receive childhood rubella vaccinations. In addition, some municipalities are offering free vaccines to women who may become pregnant and their families, in order to curb potential (visual, auditory, and cardiovascular) birth defects.


We have just begun learning about viral structure and function in class, and how (for lack of a better term) virulent they can be. Rubella is another example of an airborne pathogen, and it was thankfully eradicated from the US in 2004, according to the CDC.

Critical Analysis:

This, as with other similar stories from NHK World, are meant as informative public broadcasts rather than in-depth scientific literature. It focuses mainly on raising public awareness of, and government response to, the outbreak. It does, however, touch on the complications rubella can present for pregnant women.


How prevalent are airborne viruses, and why is everyone not infected all the time by an airborne pathogen without the biological constraint to maintain life?

Additional Info:


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

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’?

A2: Pigs culled in Shiga after swine fever outbreak

NHK World, 2/07/2019

Summary:  Roughly 700 pigs have been culled at a farm in Omihachiman, Shiga Prefecture (滋賀, middle left on map) after an outbreak of  Pestivirus CSFV, a Group IV virus responsible for classical swine fever. While this pathogen is highly contagious among domestic and wild swine and known to cause symptoms including fever, skin hemorrhaging, convulsions, and death [1], humans are not susceptible. The carriers were among a total of 60 pigs shipped from Aichi Prefecture (愛知, center bottom) to four other prefectures on January 31st. The first case of CSF in Japan in 27 years was discovered September 2018 in Gifu Prefecture (岐阜, center top), spreading from there.


While we have not yet covered viruses or communicability in class, the precautions we take in lab to avoid communication of our unidentified strains is likely an afterthought on commercial farms. It’s no wonder that crafty and deadly pathogens could have such a devastating effect on food supply chains.

Critical Analysis:

This article is written more as an informative story than a piece of scientific literature. However, it does provide reliable information on what  Pestivirus CSFV is and the effects it can have. While it has been reportedly eliminated in many western countries, including America, Canada, and Australia, cases still arise such as East Anglia, United Kingdom in 2000 [1].


What makes pathogens selective in their attacking, and is it truly more advantageous to specialize and “hide under the radar” rather than diversify to obtain the maximum potential number of hosts?

Additional Info:

[1]:  https://en.wikipedia.org/wiki/Classical_swine_fever

A2: Microbes in the News Assignment

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



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.