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.

A2: Microbes in the News Number 3

“Scientists discover how ‘superbug’ E. coli clones take over human gut’


by: University of Birmingham (no author listed)

April 23rd

Link: https://phys.org/news/2019-04-scientists-superbug-coli-clones-human.html


Research was done on a strain of E.Coli that is resistant to many drugs, and why it has become a source of infections related to the bacteria. The amount of E.Coli cases has risen 27% between 2012-2013 and 2017-2018. The researchers said that the reason it has not become completely dominant is because if there is only one strain of E.Coli and something happened to that strain then E.Coli would disappear. They said Negative frequency dependency selection keeps balance in E.Coli populations so this does not occur. It also mentioned that this strain of bacteria had a lot more variability genetically in genes that help colonize the gut than other strains.


This connects to what we learned in class because it talks about drug resistance in bacterial species.

Critical Analysis:

I think that it is interesting that the amount of E.Coli cases has risen as much as it has. I think this article is credible as it cites from the authors of the paper it talks about. I think this article did an okay job at explaining to the public, there were a couple of terms they could have described further to make it make more sense such as negative frequency dependency selection.


How is it possible that one specific strain could become so much more dominant than other strains of E.Coli?

Microbes in the News – #3


The CDC has warned healthcare facilities in the United States about an outbreak of a resistant super fungus spreading across the United States, so far twelve states have seen outbreaks, with over 600 people infected.

A resistant strain of Candida auras  has killed half of the people infected within ninety days of contraction of the fungus. The outbreak has been associated with hospital stays and is cause for concern as a global emerging threat as a superbug due to it’s resistant to multiple anti-fungal treatments and all antibiotic treatments. It presents with vague symptoms; including general malaise, fever and chills. People with weakened immune systems are the most vulnerable, however, the outbreak is of great cause for concern if it has not been cured; at which point the potential for infection would pose a threat for infection to healthy people with healthy immune systems.

Candida auris is a yeast discovered in 2009 in Japan, after which time infection spread across Asia and the Middleast and entered the U.S. in 2013.


In class we have studied fungi and leaned that infections are difficult to treat because they are Eukaryotes and treatment could pose damage to our own cells.

Critical Analysis:

I think the news clip was a great way to get quick information, however, I do not think that it would be the best way to learn sufficient information regarding the topic and the reason why it would be of concern. Also, I think that including a medical perspective was a great idea because she provided an informed discussion.


The medical doctor mentioned that Candida auris is a normal part of the gut micro biome, however, when I checked other sites, I could not find supporting documentation. Is Candida auris a normal inhabitant of the human gut?

Article and Link:

CBS News (  2019, April 19). CDC warns about mysterious “superbug” fungus.  Retrived from https://www.youtube.com.

Candida auris. (n.d.). In Wikipedia. Retrieved 2019, April 23, from https://en.wikipedia.org/wiki/Candida_auris

Microbes in the News #3 – A Changing Ocean (Sage Robine)

Article:  Study: Much of the surface ocean will shift in color by end of 21st century

(https://news.mit.edu/2019/study-ocean-color-change-phytoplankton-climate-0204) –> MIT News, February 4, 2019

Summary:  Researchers at MIT have developed a model that simulates how the colours of the ocean may change over the next 100 years due to climate change. Their model looks at the colours of the ocean as seen from a satellite, where green hues indicate a greater concentration of algae and phytoplankton while dark blue hues indicate a lack of significant algae growth. Their model predicted that the subtropics will turn a deeper blue colour, indicating less phytoplankton growth and therefore less life in general. Meanwhile, the poles may turn a darker shade of green from increased algae blooms due to warming temperatures. These changes in levels of algal growth mean that entire food webs could be significantly altered by the end of the century, which would have significant impacts worldwide.

Connections:  This article is a good reflection of how microbial ecology can have a big impact on our world. Changes in microbial activity in the oceans over the next century could be big enough to be seen from space! And since life in the ocean is very dependent on levels of microbial growth (microbes make up the base of most ocean food webs) these changes could have dramatic impacts on all domains of life.

Critical Analysis:  I really enjoyed reading this article. It was easy to read and seemed to summarize the MIT study really well. I am somewhat cautious about this model, because I have not seen proof of its face and predictive validity, but I am sure if I read the entire peer-reviewed paper in depth it would prove to be a fairly accurate model for ocean colour change. Overall, this article was well-written, informative, accurate and easy to understand.

Question:  If the algal growth in our oceans changes as much as it is supposed to, how can we model these impacts on ocean food webs and what would those models show us?

Third Microbes in the News

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

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?

Sarah Brower Microbes in the News 2

Biological characterization of  Pasteurella multocida  present in the Saiga population

by Mukhit Orynbayev, Kulyaisan  Sultankulova, Abylay  Sansyzbay, Rashida  Rystayeva, Kamshat  Shorayeva, Aidar  Namet, Sasan  Fereidouni, Gulnaz  Ilgekbayeva, Kainar  Barakbayev, Syrym Kopeyev,   and Richard  Kock



P. multocida is a commensalist in human upper respiratory tracts.   from 2010 to 2015 there was a large mortality event among antelope in West Kazakhstan and Kosnstay.   They dies of hemorrhagic speticimia of a bacteria later identified through 16s ribosomal RNA sequencing as P. multocida.   These bacteria are stable commensals and opportunistic pathogens.

This paper was published two months ago, and I thought it was quite timely, considering it gives examples of both commensals and opportunistic pathogens.

I wonder how widespread some of these microbes can be?   These antelope had been followed for 40 years, and there was very little genetic diversity.   How can a microbe infect so many different forms of life and be the same, down to the subspecies.

A2: Microbes in the News (#2)

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?

A2 Microbes in the News: Post 2

Title: New technique pinpoints milestones in the evolution of bacteria.

Jennifer Chu, February 7, 2019.

MIT news


Summary: A new technique has come up that will allow scientists to better determine when various species of bacteria evolved. This stemmed from a published paper that determined some groups of soil bacteria developed the ability to break down chitin 450-350 mya. They believe that this evolutionary change was caused by the changes occurring in other species, that were evolving and leaving behind chitin in the soils. Gregory Fournier claimed that tracing similar genes could allow them to find out more about animal history. There is no fossil record, so scientists have been using a molecular clock to determine when mutations were occurring. They also claim that they can use other species with clearer fossil records to determine when evolution of certain traits passed to the species they are interested in because of phenomena such as horizontal gene transfer. The scientists were specifically interested in learning about chitinase, because it is seen in most bacterial groups and fungi (whom apparently have a good fossil record). They created trees showing the relationship between all the species they chose based on genetic mutations, then used the molecular clock technique to determine when the species with chitinase diverged.


This connects to what we’ve learned about in class because it discusses horizontal gene transfer.

Critical analysis:

I think it is interesting that this is considered a new technique, I thought they had already been doing this kind of research, but maybe they had just not found a way to do it in bacteria. I think the article was scientifically accurate, based on the fact that is cites an actual published paper that was funded by NSF.  I think it was written well, it seems to be in a language that most people might be able to understand if they have some sort of previous knowledge or interests in science, however if they don’t they might be confused by some of the terms used within the article.

Question: Would this research about the evolutionary history of microbes possibly be helpful in further understanding the concept of horizontal gene transfer, and maybe be helpful in fields such related to infectious diseases, so they could trace when the negative genes were transferred?

A2: Microbes In The News-Antibiotic resistance and ROS treatment

Title: “Anti-evolvability drugs could slow antibiotic resistance in bacteria.”  

Depiction of E. coli response to low doses of antibiotics causing sub-populations with different responses to emerge. Credit: John P Pribis

Publisher: Cell Press

Link: <www.sciencedaily.com/releases/2019/04/190401115806.htm>.

Published: April 1st, 2019

Summary: Growing antibiotic resistance is a threat. Traditionally the focus is to develop new antibiotics. This article focuses on identifying a mechanism by which drug resistance forms and identify a drug that prevents the mechanism from developing antibiotic resistance. In this case researchers observed that low doses of ciprofloxacin (“DNA breaking” antibiotic) administered to E. coli caused a stress response in a fraction of the isolate population which resulted in high levels of reactive oxygen species (ROS) production. Which in turn, induced error prone DNA repair. This particular stress response strategy relies on a sort of mutation gambling that results in the rapid evolution of new antibiotic resistance without risking the entire microbial population. ROS-reducing drugs exist and are approved by the FDA for other uses. Researchers exposed E. coli to low dose ciprofloxacin and ROS-reducing drug edaravone in tandem and successfully prevented the formation of new antibiotic resistance in their tested E. coli populations.

Connection: Class covered how antibiotics treat bacterial infection. Bacteria develop antibiotic resistance for a variety of reasons as discussed in lecture. Antibiotic resistance prevention we discussed fuocused mainly at prevention of resistance development. Mechanisms by which resistance forms were also discussed but this idea to inhibit resistance mechanism during antibiotic treatment is quite clever.

Critical analysis: ScienceDaily is a reputable and credible news source. This story directly cites the original journal article and states its content is edited for “style and length”. This sort of reporting is perfect for casual scientific reading. It makes reading easy unlike reading the original journal article while staying completely factual and referenced. The perfect middle ground between deciphering a scientific journal article and reading a very watered down interpretation of the article in a non specialty news publication.

Question: What other mechanisms do bacteria use to develop antibiotic resistance? How could the mechanism you thought of be disrupted?