So Happy Together

Isolation and Characterization of

Sphingomonas paucimobilis and Bacillus amyloliquefaciens

from Household Kitchen Faucet Aerator

MM Ragusa

Here I characterized two bacteria species isolated from a sample from my kitchen faucet, and experimented with how they interacted with each other.

Bacillus amyloliquefaciens (left) interacts with Sphingomonas paucimobilis (right). S. paucimobilis forms yellow, isolated colonies, which are completely overgrown by B. amyloliquecaciens.

Art Project

Building the HPV Capsid


Style:  visual arts

Medium:  modelling clay


Research: virions, capsomeres, capsids, HPV capsid, geometric symmetry in nature.

Conceptualizing: Modelling clay allowed a space-filling construct which could be used to show organizational elements. This also allowed me to create the functional purpose of a jewelry or knickknack box.

Construction: Once I picked a shape to represent capsomeres (small spheres), it took some time to make 360. Unfortunately, there was limited surface area on each sphere to prep for connection scoring. They became distorted as I “mooshed” them into neighbors. In this respect, this model poorly represented the spaces naturally occurring between capsomeres in a capsid. I then assembled the clusters into arrangements of six clusters. Assembled, each half of the functional piece contained six arrangements of six clusters. Notably, my capsomere clusters were arranged as 2D pentagons. This is not an accurate representation of how the natural proteins would assemble. The conformation of each naturally occurring cluster is consistent with other clusters, however, which I did reflect here.

Microbiology Concept:  I explored the symmetry found in nature. In this case, my reference was abiotic, but certainly found in nature and microbiology. I tried to build an icosohedral capsid reflecting the arrangement of proteins in the HPV capsid. I was intrigued by how 72 capsomere clusters could be symmetrically divided between 20 faces, while still reflecting the 12 vertices as points rather than non-specific areas. I wanted to show how even non-geometric shapes such as proteins could demonstrate geometric symmetry when arranged in repeating patterns. As an aside from symmetry, I demonstrated the “hollow” nature of the capsid shell around nucleic acid by showing both circular and linear genetic elements inside the opened model.

Cluster of 5 Capsomeres
72 Clusters of Five Capsomeres
Assembled Capsid
Opened Capsid with Circular and Linear Genetic Elements


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:


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).

A6: Painting with Microbes

Name/ Section : MM Ragusa/F03

Color by Colony


Artistic Intent:

I surrendered the attempt to create beautiful art for the purpose of demonstrating how media can impact the feel of an image. My inspiration came from watching crows above the snow laden tree in my front yard on a cold, sunny afternoon. Contrast and complimentary colors create an open, high energy feel, as seen on the top plate pictured below, most representative of my inspiration. Using a background media which doesn’t contrast, or changing the color of shapes so they are similar shades to the background can either result in a fuzzy, unfocused feeling, or in an intense, turbulent feeling. These may be seen in the middle and bottom plates, respectively.


Each agar plate is painted with three different microbial organisms. The cloud on each is painted with Serratia marcescens, a Gram-negative non-fermenter. The birds are created with Chromobacter violaceum, another Gram-negative non-fermenter. The treetop at the bottom of each plate is made of Enterobacter aerogenes, a Gram-negative fermenter.

Role of Media in Color Spectrum

On the top plate the media is Tryptic Soy Agar (TSA), a standard complex medium. The background on this plate remains a neutral color, and microbes growing on it develop colonies which are colored by their natural pigments (pink for S. marcescens, deep violet for C. violaceum, and white for E. aerogenes). The cloud on this plate is a very light pink, typical of a young colony of S. marcescens.

The middle plate is Eosin Methylene Blue (EMB) agar, a medium which is selective for (does not inhibit the growth of) Gram negative microbes. EMB   is also differential, in that it changes in response to fermentation products. Lactose and sucrose fermentation create acidic products, which turn eosin red or black. By consuming the medium, strong fermenters turn black with a metallic green sheen. If the organisms ferment but produce less acid, they turn pink to red on EMB agar. This can be seen in the light pink hue of the tree top on the middle plate. (I had hoped for stronger fermentation effects.) Non-fermenters should retain their original colors. The microbes on this plate found something delicious, and overgrew in just 17 hours of incubation after being painted on the EMB agar. The microbes in the birds were out-competed for the limited resources on the plate.

The bottom plate is MacConkey (MAC) agar, which is also selective for Gram-negative microbes and differential in response to fermentation products. MAC agar contains peptone rather than sucrose, in addition to lactose. The pH dependent dye in MAC agar lightens to pink from the products of lactose fermentation. Again, this is seen in the pink hue of the tree top on the bottom plate. Non-lactose fermentation lightens the agar even further, and produces white or colorless colonies on light pink to translucent agar. None of the microbes used were non-lactose fermenters, so the agar has only a halo of lightening around the tree top. The pink color of the cloud on this plate is not explained by the plate’s differential nature, as non-fermenters should retain their original colors. The darker pink is more representative of mature S. marcescens colonies. The C. violaceum grew colonies only in the most densely painted parts, perhaps in response to some agar quality.


A3: Epithet Epitaphs


Microbial Species:

Gulbenkiania mobilis

Genus Namesake:

Calouste Gulbenkian

Latin Binomial:

mobilis; movable or motile

Brief Biography:

Calouste Gulbenkian was born March 23, 1869 in what is now Istanbul, Turkey. His father was deeply involved in oil import/export. After Calouste’s education in Armenian and French schools, he studied at Robert College in Istanbul and King’s College in London, earning a degree in petroleum engineering. Following his father’s footsteps, he started his own oil operations business in 1895. The next year he fled the Armenian Massacres and formed a network of wealthy and influential contacts in Egypt. He then moved to London and conducted business deals with the aid of his contacts. He arranged mergers and developed multiple oil companies, most notably the Iraq Petroleum Company. His role in the development of that company and others resulted in his nickname, “Mr. Five Percent.” The retention of five percent of the shares of companies he handled fueled his massive acquisition of wealth. As a billionaire, he owned several homes and amassed a huge art collection. He also donated millions of dollars, mainly to Armenian establishments. He was a benefactor to churches, hospitals, a library, and to settlements for refugees from the Armenian Genocide. Gulbenkian spent the last thirteen years of his life in Lisbon, Portugal, and willed a large portion of his fortune to the establishment of the Calouste Gulbenkian Foundation there. The Foundation promotes arts, charity, education, and science throughout the world. Much of Calouste’s art is housed at the Calouste Gulbenkian Museum in Lisbon. At his death in 1955 he was reportedly the world’s richest man.


Calouste Gulbenkian. (2019). In Wikipedia. Retrieved January 27, 2019, from

Calouste Gulbenkian Foundation. (2019). Last Years in Lisbon. Retrieved January 27, 2019 from

Conlin, J. (2019) Mr. Five Per Cent: The Many Lives of Calouste Gulbenkian, the World’s Richest Man. [Kindle Editions version]. Retrieved from

A2: Microbes in the News

Article and Link:

Microbes Might Be Key to a Mars Mission

Engineered yeast could turn waste into food, plastics and other essentials

By Mark Blenner on January 14, 2019

Microbes Might Be Key to a Mars Mission

Image Credit: NASA, Clouds AO and SEArch Wikimedia

Blenner, M. (2019, January). Microbes Might be Key to a Mars Mission.  Scientific American.  Retrieved from


The author describes the work of his team as they engineer modified versions of the yeast  Yarrowia liplytica.  Dr. Blenner suggests strains of the modified yeast could survive on waste products from astronauts while creating materials to facilitate repairs and improve astronaut health. Genes “borrowed” from other organisms could allow the modified yeast to generate useful products. For example, these products could be used as the building blocks for 3-D printed parts or for adhesives used for repairs. One strain of the modified yeast uses genes “cut and pasted” from plants and algae to produce eicosapentaenoic acid (EPA). This valuable Omega-3 fatty acid is a neutraceutical known to help prevent bone density loss in astronauts.


In lecture, we discussed yeast as a model species. This organism is often mistaken for a prokaryote by new biology students, perhaps because it is small and single-celled. These fungi have a membrane-bound nucleus, however, and are thus eukaryotes. Use of yeast strains as model species predates work begun by Dr. Blenner in 2012.

In lecture we also touched on synthetic biology, and its similarity to traditional genetic engineering. In genetic engineering, genes known to code for products resulting in desired traits are “added to” an organism’s genome. The desired traits referred to in this article are: 1) the consumption of astronaut waste products and 2) the production of products useful to astronauts during space travel.

Finally, a Microbes in the News article posted by @kcallegari discusses the hardy nature of microbes found in the International Space Station (ISS). I think the evidence of mutations in the bacteria found in the ISS may have applications in the engineering of the yeast strains Dr. Blenner’s team is working with. I think it would be interesting to consider what mutations are already present in the “space generations” of bacteria, and what might happen if similar mutations occur in modified fungi.

Critical Analysis:

This blog was written in a conversational, non-jargon language which made the main points easy for anyone to understand.   Dr. Blenner referenced a recent scientific publication, and gave a one-sentence summary of those findings (Brabender 2018). He then connected this to his current research, which validated the need for this avenue of investigation. This was effective scientific communication because raising awareness of potential benefits to this area of study is the best way to bolster interest and thus funding for further research.

I felt there was some implication that the products from the modified yeast strains were sure to be useful to astronauts, which isn’t supported by the findings he presented in this article. However, I can understand that determining how to harvest and utilize those products and proving that the processes would be worth the time and tools it might take wasn’t the purview of the current study. This may be the next stage of study for his team, or may be the task for another team of scientists. Perhaps acknowledging the limitations of the current study may have made the need for future supporting studies seem less glossed-over.

I thought citing his background in studies of synthetic biology and yeast helped to authenticate Dr. Blenner’s article, as did his bio, which notes the funding source for the current research. In all; the article identified a real-world need, referenced published scientific literature, explained how the current study aimed to address the real-world need, and suggested potential benefits of further study. It was an effective use of the blog forum to garner awareness and potential support both for his team’s current research and for future studies.


I understand scientists use model species because these species have characteristics universal enough to apply to other species across the tree of life. In the studies this article describes, the DNA regions of interest being transferred are from simple organism to simple organism. The regions cut and pasted into other organisms’ genomes can include one gene or several genes, as well as parts of the non-coding regions surrounding those genes. This may have relatively straightforward results in single celled organisms. Yet in multi-celled organisms, there are innumerable inter-systemic interactions in the micro-chemistry unique to each species. For example, a single neurotransmitter can affect both brain chemistry and gut processes (Li 2004). Is it productive and ethical to experiment with inserting regions of interest into more complex species before the biochemistry of inter-dependent bio-systems are fully mapped out?


Brabender, M., Hussain, M.S., Rodriguez, G. et al. Urea and urine are a viable and cost-effective nitrogen source for  Yarrowia lipolytica  biomass and lipid accumulation. Applied Microbiol Biotechnology (2018) 102: 2313.

Li, Z.S.,  T. D. Pham,  H. Tamir,  J. J. Chen  and  M. D. Gershon.  Enteric Dopaminergic Neurons: Definition, Developmental Lineage, and Effects of Extrinsic Denervation.  

A1: Introducing Maggie

Hello All. My name is Maggie. Please don’t mind me when I sign off   with “MM Ragusa.” Old habits die hard, and I learned a long time ago that a little ambiguity can reduce a lot of judgement. So I like to keep ’em guessing…

I saw some of the Painting with Microbes pieces from previous semesters, and I was interested in how it was done.   Here’s a You Tube video, in case you’re interested too. Some of it is truly amazing artwork! I have no aspirations of creating anything more impressive than a smiley face, but it’s awesome to see what can be done, when you know your medium. (In this case, the medium is microbes!)

Here’s the winner of the 2018 American Society for Microbiology’s Agar Art contest:  “The Battle of Winter and Spring’ by Ana Tsitsishvili.