All That Public Services Have To Offer: The Little Company of Microbes You Do Not See


Chelsea Brown

28 April 2017

Bio 342 F01


All That Public Services Have To Offer: The Little Company of Microbes You Do Not See


There is a great dependency on public services: public schools, public bathrooms, and public transportation. Here, almost everyone is welcome to use the facilities provided. However, it is not only people that are clustering in these locations. Having so many different people coming together all in one place provides the perfect environment for microbes to gather. The definition of a microbe is still being debated today. However, for the sake of this research, we will go with the Brock Biology of Microorganisms definition: microorganisms are a microscopic organism consisting of a single cell or cell cluster, also including the viruses, which are not cellular (Madigan et al.).

As an avid user of public facilities, I chose to isolate, characterize, and identify a bacterium from the Fairbanks city bus. I retrieved my sample during the winter season when the common cold and flu was rampant through the city. Most bus users were the elderly or the working class or less common, college students like me. I was curious to find out what microbes we were all coming in contact with, I hypothesized it would be a bacterium or virus that could make you sick. After some observation, I realized most riders would use the poles in the bus either to help themselves on or off the bus. This bar is where I swabbed approximately two-inches with a damp cotton swab. I then streaked a TSA plate and kept my culture in a room temperature environment until further study which included: isolating my bacterium, running tests to find certain traits of my bacterium and finally obtaining its genome sequence.

The data of my bacterium brought me to the conclusion that I had Pseudomonas aeruginosa. Pseudomonas aeruginosa is described as an opportunistic pathogen found both inside and outside of the human body. It is an important bacterium for its multidrug resistance, antibiotic resistance, and association to diseases (Friedrich, 2016).


I chose my sample site on the Fairbanks, Alaska city bus. I used sterile swabs dipped in DI water to collect my sample from a one inch section of the hand bars near the front of the bus. I then streaked my TSA Plate and kept it in a dark and room temperature environment, approximately 75 degrees Fahrenheit. After five days, culture began growing on the plate. The plate had three different colonies growing in the same area. I chose an isolate in the middle of the colonies and streaked a plate using the four quadrant streak method. I followed the protocols of sterilization as provided in Lab 2 Handout. My plate was kept in an incubator set at 37 degrees Celsius. After 48 hours, I streaked another plate using the same method and repeated this process four times.

After obtaining a pure culture, I used the gram stain test to find if my bacteria were gram positive or gram negative. This test is the first test I ran to place my bacterium in a morphological group. I followed the gram stain protocol in Lab 4 Handout: Staining Techniques. After staining, viewing my gram stain slide under a microscope would also allow me to see the morphology of my cells.

I then began growing my pure culture in an agar slant tube. The slant was kept in an incubator at 37 degrees Celsius before being moved to the refrigerator at 4 degrees Celsius after the culture had visibly grown after a week. The next week and API 20E test was done on my bacterium. The API 20E test strip tested for twenty different characteristics of my bacterium. Some tests included GLU which tests if glucose is used which it usually is. The test trip protocol I followed was provided in Lab 6 Handout and I then incubated the strip at 37 degrees Celsius for 24 hours. Further tests included the fluid thiogylcellate test, the oxidase and catalase test, and the genome sequence test. The oxygen status whether it is aerobic or anaerobic is told by the fluid thioglycellate test. The oxidase test I ran was would tell me if there is cytochrome c oxidase was present or absent. It would also tell me if my bacterium can use oxygen as a terminal electron acceptor in respiration. The catalase test would tell me if this enzyme is present, the presence of this enzyme means my bacterium is protected from oxidative damage.

Ian Herriott, a technician in the Institute of Arctic Biology DNA Core Lab, performed the whole genome sequencing on the genomic DNA of my isolate on Ilumina MiSeq. Through a series of steps reported in Lab 7 Handout, my sequence is provided and analyzed in a computer program called “BaseSpace’. Through the app “SPAdes Genome Assembler’ I was given information on my bacterium’s contigs and the app “Kraken Metagenomics’ gave me its taxonomic classification.

The final test done on my bacterium was to test its susceptibility or resistance to antibiotics. I chose six antibiotic discs at random to test. I split two TSA plates in sections of three. I followed the protocols in Lab 9 Handout to test my bacterium for antibiotics.




Figure 1. A quadrant streak of my experimental culture. This shows a pure culture on a TSA Plate.


Figure 2. A 1000X light microscopic view of my experimental bacterium after a gram stain test.

Figure 3. An API 20E Strip results after 24 hours. From left to right the tests are: ONPG, ADH, LDC, ODC, CIT, H2S, URE, TDA, IND, VP, GEL, GLU, MAN, INO, SOR, RHA, SAC, MEL, AMY, ARA.






The gram stain test’s outcome was gram positive. In addition to my bacterium being gram positive, I saw the morphology of my bacterium was rods where some were coupled and some were in clusters. The cell size was roughly 0.6 by 1.5 micrometers.

The API 20E test had negative results in every section: ONPG, ADH, LDC, ODC, CIT, H2S, URE, TDA, IND, VP, GEL, GLU, MAN, INO, SOR, RHA, SAC, MEL, AMY, ARA. The API20E test appeared invalid as some of the wells appeared to have dried out. The first and second test of the fluid thioglycellate did not yield any result for my microbe. There was no bacterial growth to be seen in the broth.

The results of the catalase and oxidase tests were both positive: Bubbles forms when Hydrogen Peroxide was dropped on my bacterium sample for the catalase test. The genomic sequencing software gave a species name, Pseudomonas Aeruginosa with a 99.15% reads classified species level. Finally, my bacterium did not grown on the TSA plate for this and therefore yielded no results.



Apart from the inconclusive tests, all tests corresponded to the literature on Pseudomonas aeruginosa. Pseudomonas aeruginosa is a very common bacterium often characterized as an opportunistic pathogen (Juhas et. al, 2005). Though I did not find my isolate in a mucous or water environment, it is not unusual for my bacterium to adhere to metal surfaces in a biofilm. Finding my bacterium on a public bus hand bar was consistent to its preferred environment. However, where my bacterium was finding its food source is still in question. This is a study I could go further into.

  1. aeruginosa is a gram-negative rod shaped bacterium which was analogous to my morphological tests. The expectation was that my bacterium needed oxygen considering the location of where it was found. The positive results from my catalase and oxidase tests were also conclusive with to my prediction. The one thing that was not correspondent was P.aeruginosa’s motility. However some sources said it could be both motile and immotile (Campbell, 1994). Since my isolate was not found in water, it is possible I sampled a colony in a biofilm state (Tiedje, 2007).

Pseudomonas aeruginosa proved capable of growing in all of the mediums used for the experiment except the agar used in the thioglycellate test. I still do not know why my bacterium did not grow the two times that I conducted this test. It is possible the culture I used to inoculate the broth for the test was no longer active. I should have made a fresh culture for the test. P. aeruginosa can grow in the Mueller-Hinton agar but may have been unsuccessful due to the poor preparation in growing the pathogen in the broth before applying it to the plate. However, after some research, I found my bacterium would have been resistant or partially resistant to all of the antibiotics (Friedrich, 2016).

Some wells on the API 20E test strip, such as those for mannitol fermentation and gelatin hydrolysis, should have been positive (Aryal, 2015). As was the case in my fluid thioglycellate test, it is possible my bacterium was not grown enough in the medium I used to fill the wells. As time went on during these tests, I may not have revived my culture enough and it could have gone dormant. In the future, it would be best if I prepared a fresh plate before every test. Further, I could do additional tests such as seeing how long my isolate would survive in various kinds of environments without a constant food source.


Though there were insufficient results from human error, through the genome sequencing results and successful tests, I was convinced that I did indeed have Pseudomonas aeruginosa. I had a high confidence interval on the “Kraken Metagenomics’ app with few other results coming close. P. aeruginosa is a common bacterium found in many locations and the probability of coming across it is plausible. However, P. aeruginosa is mostly found in hospitals, which does lower my credibility since I did not swab my sample from a hospital. It was exciting and weary possibly finding such an opportunistic pathogen in the location I did. Now that I am informed that microbes like these are ubiquitous, it gives a new light on the importance of washing your hands.




1.             EHA. What is Pseudomonas aeruginosa?. 2017.

2.             L. Wiehlmann et. al. “Population structure of Pseudomonas aeruginosa.’ PNAS. 2007.

3.             M. Campbell. “Nonmotility and phagocytic resistance of Pseudomonas aeruginosa isolates from chronically colonized patients with cystic fibrosis.’Infect Immun. 1994.

4.             M. Friederich. “Pseudomonas aeruginosa Infections  Medication.’ MedScape. 2016.

5.             S. Aryal. “Biochemical Test and Identification of Pseudomonas aeruginosa.’ Microbiology Info. 2015.

Assignment ll: Microbes in the News

Can airborne viruses survive in water?

This article discusses an equine herpes virus and its ability to survive in water. This causes a problem for shared water among animals. It also gives insight into viruses that can survive outside of their preferred conditions.

The first thing that came to mind after reading this article is the infectious game we played with the beach ball. This was the same lecture we talked about possible ways an infection can be passed: airborne, contact. However, for me, a combination was never considered.

An airborne virus also being able to survive in water makes the area spreading of that virus that much wider. The article mentions that even when the animal with the virus is absent, other animals were getting the infection through the shared water. This is important because trying to maintain the spread of an infection is only possible when you know all of the pathways of infection.

My question is: Have viruses always been able to survive outside of their ideal environment?

Assignment ll: Microbes in the News

Bacteria’s DNA fingerprint suggests it could be spreading via food distribution

This article discusses the spread of Clostridium difficile, a microbe that causes gut infections. C. difficile  is an important topic of discussion because it appears to be transmitted through food, resistant in some people, seen in a lot of hospitalized patients, and it can be dangerous. To track the source of this bacterium, scientists have been using DNA fingerprinting. Dr. David Eyre, the researcher of this topic, has been promoting washing hands to prevent the spread however, he thinks it is beyond this because there are different strains appearing together in different countries.

This topic ties into a couple of our lectures. We’ve discussed resistance, the human microbiome, and washing hands (soap) as being a way to kill bacteria.

I find this topic important especially since Clostridium difficile appears to be widespread and affecting certain countries. DNA fingerprinting is a great method for finding the source of a spread and I think if scientists continue to practice this kind of research we could get to a place where we can stop a disease before it begins.

My question for you is: Will this be good enough? What other ways can we prevent the spread of an infection?


Art Project: The Lytic Cycle

The Lytic Cycle Shown Through Dance

I knew from the beginning I wanted to incorporate my microbiology project with pole dance however, none of the topics seemed to easily transition into a dance. When we learned about viruses, I knew I had found my topic. I came up with a routine and asked a few girls at my studio to do it with me. Fortunately, they agreed! Unfortunately, I was asking them to give up their time and work without pay. However, they were very generous and in the short amount of time we had, I was able to show them the routine and this was only take two!

The dance starts with the “cell” being the first two dancers on the pole. Then the virus shows up on the pole (attachment). The scarf dropped down from the girls portraying the virus to the girls on the floor portraying the cell represents the DNA (DNA entry). The girls that then come into the routine is representing the virus duplicating and the floor work of the cell on the floor is its slow demise (synthesis and assembly). Finally, the virus bursts through the cell (release), ending the cycle.

A2: Microbes In The News

Better than nature: Artificial biofilm increases energy production in microbial fuel cells

12 April 2017

Scientists Prof. Dr. Ruth Freitag and Prof. Dr. Andreas Greiner have developed an artificial biofilm that can perform better and is more stable than the natural biofilms that collect in a fuel cell. The scientists felt this was a positive development because unlike natural microbes, they could control their artificial biofilm better. We’ve talked about biofilms in lecture as a convenient way for microbes to collect, grow in population size, and obtain resources without moving. Further, we discussed how microbes choose their environment, like in an oil spill. However, in a situation like the oil spill, we saw that microbes that aggregate naturally were not always the most efficient at taking care of the spill.

I found it interesting that scientists are producing artificial microbes. It made me curious if it would have been a better idea to try and obtain a greater amount of the natural microbes for the job than to make something synthetic. I feel there could be a lot of unforeseen issues that could arise such as, if this new development is safe for the environment. They did not go into great detail and I think they could have done a better job of explaining what this new development entails.

My question goes with my earlier thinking: What possible outcomes (negative or positive) could come from this development?

Extra Credit: Microbial Worlds

The art piece I found compelling was by Jennifer Moss. It was a digital photograph of a tree on vinyl. As a lover of music and vinyl records, I was drawn just by the look of her work. I thought it gave it a creative edge and was a unique way to display a piece. The angle, on the ground looking up, of the shot made me feel rooted and therefore one with the microbes around. As a microscopic view of microbes taking place of the sky, it reminded me microbes are everywhere and made me feel that much more surrounded by them.

“De:composition’ by Stephanie Rae Dixon and Mary Beth Leigh was a live art piece where a woman moved in a small box amongst leaves and dirt and other tree matter. The concept was in the name, decomposition, and how microbes help this process. This piece was especially appealing because of a projector that projected the spot with a forest surrounding making one feel like they were in the piece. The piece was enticing and a riveting way to describe decomposition with a body amongst a representation of a part of a forest.

Margo Klass’s “Specimen’ related to our human microbiome lecture. This was a series of dental pieces in poor shape. The concept was about how the human mouth has a world of microbes on its own. With the cavities and missing teeth on some pieces, it appeared he was also showing the damage these microbes can do with poor dental hygiene.

If I was an artist involved with this project show, I would have made a piece about viruses and how they invade cells. I would have created an animated piece with music fitting to an animation of a virus attacking a cell.

Extra Credit: Eric Collins

Eric Collins’ seminar was on microbial communities in the arctic. His project included mapping the uncharted diversity of arctic marine microbes. In addition to the different regions of ice, microbes were also charted by what layer of ice they were found in. Microbes in ice also vary in the age of ice and with the arctic losing old ice, microbes may be going extinct.

This seminar was especially related to lecture when we learned that microbes choose their community. Microbes in this environment chose the region, layer, and age of ice. Additionally, his research backs up the lecture that there are certain bacteria for certain temperatures and these are certainly thermophilic bacteria.

Whenever there is an organism going extinct, my first thought is always what the impact will be in its community. Since we have an understanding of the importance of microbes, it makes me curious as to what can change in the arctic with old ice microbes going extinct.

Lab 8: Painting with Microbes

This plate was my attempt to draw a turtle on the surface of water. Both bacteria I used appeared on the EMB plate and therefore were both Gram- negative. The bacteria I was using for the water fermented the sugar into an acidic product and therefore appears black and it was originally a dark pink. The bacterium I used for my turtle was originally a whitish color and since it did not ferment lactose it appears to be a light pink.

Extra Credit: Simon Lax

Simon Lax’s seminar was about microbiomes and the possibility of affiliating certain microbes to a specific person, like a fingerprint. Lax’s research on the importance of this “microbe fingerprint” came from both a forensic and health perspective. In a forensics type study, by comparing samples from someone’s shoe and the floor, Lax could essentially get an idea of who walked where. In a health study, Lax was able to see how microbes colonized in a hospital setting. Essentially, he could see how microbes in a room became more similar to the occupant over time. Further, he did a test of skin microbiomes and their relation to the patient’s diagnosis.

Our microbiology course made it clear to me that microbes are everywhere and essentially rule the world. However, I was unaware that microbes could be specific to a type of person and their environment. I always assumed microbes were random but it now makes sense that their being has some kind of order. This seminar related specifically to the lecture about viruses, specifically Norovirus, and how it is common on cruise ships. It makes sense such a segregated place such as a cruise ship would be prone to such outbreaks. A cruise ship is similar to one’s home which, as Lax pointed out, is a place where eventually everyone and most surfaces come to have similar microbes.