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?

A2 Microbes in the News


It is quite a bit older than other papers, but this article talks about a 2016 review of the stromatolites found in Iceland.   These researchers, Allwood, Rosing, Flannery, Hurowitz, and Heirwegh, believe that the stromatolites could be not biological at all, but rather a natural geological process.

This is interesting because it could rewrite what we know about the early phases of life on earth.

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

A2: Microbes in the News

Article and link: Gut microbes can spur immune system to attack cancer by Catherine Paddock, Medical News Today, and Tuesday April2, 2019 and link.

Summary: The article found that there is the a connection between a healthy gut microbiome and the ability for an individuals ability to fight tumor growth. The study conducted by Thomas Gajewski foudn that there were 11 strains of gut bacteria that can help the immune system slow melanoma growth. These bacteria assist pathways that help keep proteins table.

Connections: This connects to how lecture series on the human microbiome and how important the gut is highly diverse and assists with keeping humans healthy.

Critical analysis: I found this entire article very interesting, especially that they found specific bacteria that aid in slowing tumor growth. I’ll be interested to see how this study progresses and if they can add these specific bacteria to individuals going through cancer treatment to assist with the bodies ability to eliminate tumor growth. The mouse model study looks very promising for the transplant of the bacteria but the inflammation response seems like it might be a dangerous side effect in humans who are already going through cancer treatment.

Question: I’m wondering if there will be a way to artificially stimulate the growth of the specific bacteria without transplanting them into a host.



A2.3: Microbes in The News

Article and Link:

Hello, Little Microbe. Doesn’t This Jacket Look Yummy?

Now we can trick tiny bugs into eating our clothing. Consumption is finally a good thing.

By Vanessa Friedman in The New York Times on April 22, 2019

Image Credit: Photo Illustration by Tracy Ma/The New York Times; Courtesy of PrimaLoft (jacket).



While this article was in the fashion section of The New York Times, it concerned the modification of clothing by attaching microbe-attracting sugars to polyester fibers used in clothing. This would allow the expedited degradation of fabrics by producing a new niche for microbes, both in landfill and marine environments.


In lecture, we have discussed microbe niches, and microbial carbon sources.

Critical Analysis:

This was not a scientific article by any means, but did contain accurate information about microbial preference for less-synthetic carbon sources. While the authors report that the textile company it interviewed would not reveal “proprietary processes” for how polyester fibers would be modified, they did mention that testing of the modified fibers was being conducted over several years, and in both marine and landfill environments. For a non-science article, I thought it did a great job of identifying a problem (the massive amount of clothing taking decades to degrade), identifying a scientific solution (speeding up bio-degradation) and explaining just enough about the solution (microbes!) to make it approachable for the average fashion-section reader. I would have liked a link or reference, but like any science-minded person, I have enough to go on to look into it further. It was beyond the scope of this publication to consider concerns such as biofilms or the potential for increased infections from wearing microbe-attracting clothing. I’m sure these considerations will be investigated as these fibers move into the mainstream.


One field which has very close ties to microbiology is forensics. The microbial effects on evidence in various environments is a crucial aspect of these studies. How will a new generation of clothing with different bio-degradation rates affect this field?


Ueland, M.  et al. (2017). Degradation patterns of natural and synthetic textiles on a soil surface during summer and winter seasons studied using ATR-FTIR spectroscopy. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 185. doi: 10.1016/j.saa.2017.05.044.

A2.2: Microbes in the News

Article and Link:

A Mysterious Infection Spanning the Globe in a Climate of Secrecy

The rise of Candida auris embodies a serious and growing public health threat: drug-resistant germs.

By Matt Richtel and Andrew Jacobs in the New York Times on April 6, 2019

Medical illustration of fluconazole-resistant Candida

Image From: https://www.cdc.gov/drugresistance/biggest_threats.html



The authors write a lengthy article identifying the spread of drug-resistant Candida auris  infections around the globe. There are links, graphics, and descriptions of why antibiotic resistance is a concern, and what roles pesticides, fungicides, and agriculture play in the spread of drug-resistant microbes. The article does include lengthy discussion on the lack of publicity regarding drug resistant infections, especially in hospital settings, with C. auris infections as the focal example.


In lecture, we have addressed each of the antibiotic resistance concerns identified in this article (see summary), although lecture contained more emphasis on drug-resistant bacteria than on drug-resistant fungi.

Critical Analysis:

This article really struck home for me, as my son is serving in Kuwait, where there have been numerous fatalities linked to this infection. While less scientific in nature, the almost sensationalist tone of the article was effective in this context. Once concern or interest is evoked in the reader, the numerous links and embedded videos provide a great deal of information. Despite the likely biased perspective, I could not find any inaccurate information in the written article. It was not written with much scientific lingo, and was geared toward the average, non-science-minded individual. I’m undecided if the article crosses a line into editorial territory, as there were certainly links to creditable sources. As a whole, it may run the risk of being dismissed as an opinion piece.


We’ve discussed mechanisms for the development of drug-resistance in bacteria. Are the mechanisms used by fungi very different? If so, how?


Khan, Z., et. al. (2018, June 14). Invasive Candida auris infections in Kuwait hospitals: epidemiology, antifungal treatment and outcome.  Infection,  2018, Oct: 46 (5).

Microbes In The News-Early Life

Earliest life may have arisen in ponds, not oceans

Date: April 12, 2019

Source: Massachusetts Institute Of Technology

News Coverage: Jenifer Chu, ScienceDaily

Link: https://www.sciencedaily.com/releases/2019/04/190412115059.htm

Micro Post: Lukash Platil


MIT researchers report shallow bodies of water rich in nitrogen may have been the source of initial life on earth. These ponds, shallower then 10 cm are thought to have contained large amounts of nitrogenous oxides. Stating that oceans may have been a bad place for necessary nitrogen reactions to occur and jump start life. This idea is based on free floating RNA being present and chemically interacting with various nitrogenous oxides. Atmospheric nitrogen was most likely broken into oxide forms by frequent lightning storms and accumulated in water but nitrogenous oxide sinks on oceans would likely break down too much of the substance. Shallow ponds would have allowed for synthesis pathways to occur at a higher concentration but at a lower scale due to the low abundance of ponds on early earth.


We discussed many possibility for the origin of life on earth in class. Many origins focused on the possibility of interactions between ocean water and hydro thermal vents to create a Goldie Locks zone in which life could have spawned. We discussed what is believed to be chemically necessary for early life on earth to span. The conversion of atmospheric N2 to oxide forms and its relative abundance is what these researchers believe is the deciding factor.

Critical analysis:

I think pointing out how stable N2’s triple bond is a key factor in allowing synthesis pathways to occur. The new nitrogen sinks researchers thought of that would decrease the relative abundance of the reactive species by three orders of magnitude in oceans seems like a reasonable justification to reevaluate the location for the emergence of life. The researchers belong to MIT, the paper was published in a credible journal and the news coverage was done by a reputable, scientific news outlet.


Do you think the statistical chance of life emergence depends on the quality of environment for synthesis pathways to occur or the relative abundance of locations containing the necessary ingredients for life? i.e. Quality or quantity, which is more important?

A2: Rockland County orders public space ban for those diagnosed with measles

NPR, 4/17/2019



In response to the New York City measles outbreak, Rockland County, NY has issued an order banning those diagnosed or exposed to measles from all places of public assembly. Over 550 confirmed national cases, including 186 in Rockland and 329 in NYC, have been reported this year. This marks the second largest outbreak since 2000, the first being in 2014 (667 cases) [1]. CDC officials report that the outbreaks have been associated with Orthodox Jewish communities and other travelers returning from Israel. The vaccination rate for children in Rockland is only 72%, much lower than the 90% recommended for herd immunity to be effective.


We have covered the importance of herd immunity in class, and the dangers of an unvaccinated populace exposed to a pathogen like the measles virus.

Critical Analysis:

Though many of the Health-tagged stories on NPR have an obvious political slant, this one’s information is surprisingly clear-cut. It explains the rising toll of the infection, the cause, and the societal consequences, maintaining all this within the context of the infection.


How can the public be better informed about the benefits of vaccination and the need to take protective measures against pathogens, without victim blaming, ad hominem intelligence insults, or appealing to the cult of scientism (which would further alienate those hesitant to get vaccinated)?

Additional Info:

[1] https://www.npr.org/sections/health-shots/2019/04/15/713508519/measles-outbreak-accelerates-health-officials-warn

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?