Isolation and Identification of a Microbial Species from a College Dorm Dryer Vent


                     Microbes are frighteningly fantastic creatures. They can grow practically anywhere and can do almost anything given enough time. Microbes can even grow in dry, hot, low-nutrient environments such as on a dryer vent. Laundry rooms are generally a place where things go to be cleaned, however the vents in a laundry room often get ignored and can become particularly dusty which provides an environment for microbes to grow. A previous study done by Barberán et al found that there is a lot of variety in microbial communities living on dust and since dryer vents accumulate a lot of dust I felt as though it would give a very diverse community of microbes that I could isolate from. This is why I set out to isolate, characterize, and identify a species of microbe that can grow on these vents.

                  I inoculated a culture of mixed microbes from the vents behind a dryer machine in a college dorm and over time created a pure culture of a single microbial species and performed various tests to help identify the species I isolated. I assumed that the microbial species living on a dryer vent would be interesting to isolate because it would need various adaptations to be able to grow on metal that frequently changes temperatures where there is low nutrient concentrations. I believed that the isolate would have been able to form endospores as it would be able to solve the issues with living in the inhospitable environment where it had been taken from.

                   I predicted my isolate would be aerobic to some extent and must have some mechanisms to cope with the relatively extreme environment that is a dryer vent. The microbe isolated must also cope with periods of time where it is cold (~5 °C after a period in which the dryer is left unused) and be able to withstand living for long periods of time without water since it lives where these coping mechanisms are a necessity.



               The initial mixed culture was collected using a sterile, moist swab on the vent behind a dryer and streaking it over a tryptic soy agar plate. After swabbing the plate was left sealed in a dark, warm environment for a week before being brought to the lab. This was done because I could not culture the plate in a moist area and dark warm locations are fairly good for microbial growth. In the lab the microbial colony was chosen and isolated using the streaking method multiple times over two weeks. By streaking many times I managed to isolate the microbe and had a pure culture. When not in use, cultures were kept growing in an incubator kept at 37 °C or in a refrigerator after they had been grown for a few days.

                     After isolating the microbe I performed a Gram stain of the microbe since it is easier to classify the microbe based on whether it is Gram-positive or Gram-negative. A fresh culture of the isolate was then used for a DNA extraction. The kit used was the PowerSoil DNA kit manufactured by MoBio as it functions well for pure cultures (Lab 5 Handout). The DNA was then sent out and sequenced using the Illumina MiSeq DNA sequencer. I then performed 4 physiological tests on the isolate which consisted of a fluid thioglycolate test to determine oxygen class, an oxidase test to determine the presence/absence of cytochrome c oxidase, a catalase test to test for presence/absence of catalase for use in protection against reactive oxygen species, and an API 20E test strip that is a miniature test for 21 different physiological processes that works well for Gram-negative microbes. These tests were done to give me insight into the ability of the microbe to cope with various different situations, further narrowing the mystery that is the unknown isolate.

                  When I received the isolate’s sequence data I ran it through SPAdes genome assembler to assemble the genome of my isolate, Kraken Metagenomics which can be used to identify my isolate to the species or genus level, and Prokka genome annotation which is used to annotate the genes of my isolate and determine their function. The isolate was further tested using antibiotic discs on a fresh culture of the isolate spread over new plates. This was done to identify whether the isolate had any adaptations suited for common antibiotics.


                Performing a Gram stain revealed that the isolate is Gram positive. The isolate formed shiny, yellow, large colonies that smelled pretty foul. The isolate tested positive for catalase and was shown to be an obligate aerobe in a fluid thioglycolate test. In the API 20E test strip the isolate tested positive for oxidase only.

                   SPAdes genome assembler gave 337 contigs >=1000 bp with the largest contig of 47421, a total length of 2409415 and a GC % of 73.02%. This means there was an ample amount of contigs to be read by the next tests and that most of the genome of the isolate consisted of cytosine and guanine. Kraken metagenomics classified 99014 reads which was 82.26% of the total reads. Of the total reads, 81.23% were classified to species level and of the reads classified to species level 98.75% were classified as Micrococcus luteus. The results of Kraken also gave Figure 2 which identifies M. luteus as 80.21% of the analyzed reads. Prokka genome annotation gave 2177 coding genes for the isolate.


                 The results of antimicrobial testing revealed that the isolate was susceptible to Tetracycline, Tobramycin,Cefazolin, Trimethoprim, Amikacin, Gentamicin,Vancomycin, and Cefoperazone.

Fig 1. Colonies of the isolate after ~108 hours upper left portion of the large colony is how most fresh colonies looked.

Fig 2. Krona classification chart from Kraken metagenomics.



                   Results from genome sequencing (Figure 2) alongside all the physiological tests performed, has lead me to believe that the isolate is indeed Micrococcus luteus. Given that the isolate had an 81.23% match to M. luteus with 18% of the DNA being unclassified, it is most likely that the isolate I found was M. luteus. The isolate also tested Gram positive, and as M. luteus is Gram-positive the results support my claim. The isolate also tested as an obligate aerobe, which is yet another reason why the isolate is likely M. luteus (Woodward and Douglas 1991).

                   The identity of my isolate is congruent with where I collected my sample and the literature supports how it existed in the environment of a dryer vent. M. luteus is known to live in dusty environments and has mechanisms to survive extreme changes in the environment that would come with living on a dryer vent (Kaprylants and Douglas 1993). Unlike most other bacteria M. luteus does not form spores, but instead can become dormant and return to normal when conditions are favorable (Greenblatt et al 2004). This adaptation would provide a way for the isolate to have lived with the changes that come from turning on the dryer and heating up the otherwise cool vent. The isolate would also have been fine without having methods to deal with chemicals as the vent behind the dryer is not normally cleaned and spends long periods of time without being exposed to chemicals that could kill M. luteus. As M. luteus, the isolate would be able to survive extended periods without food and various temperature changes that come from living on a dryer vent all while avoiding the need to survive harmful cleaning chemicals.

                    That being said, the isolate tested positive for catalase which may mean that even though the isolate would survive all aforementioned conditions the isolate still needed the catalase gene to prevent reactive oxygen species from harming it. That would make sense as reactive oxygen species would likely interfere with the survival of M. luteus as the oxygen species would likely interfere with cell structure and function if there was no catalase gene. This means that the catalase gene could be necessary for the extended dormancy period of M. luteus or that the isolate was exposed to enough reactive oxygen species existing on a dryer vent that catalase was an important gene to have. The isolate was also susceptible to the antibiotics I tested on it, which makes sense because the isolate lived in an environment that was likely free of antibiotics and would have no use for antibiotic resistance genes.


Works Cited

Barberán, Albert, et al. “The ecology of microscopic life in household                dust.” Proc. R. Soc. B. Vol. 282. No. 1814. The Royal Society, 2015.

Greenblatt, C. L., et al. “Micrococcus luteus-survival in amber.” Microbial            ecology 48.1 (2004): 120-127.

Kaprelyants, Arseny S., and Douglas B. Kell. “Dormancy in stationary-                  phase cultures of Micrococcus luteus: flow cytometric analysis of              starvation and resuscitation.” Applied and Environmental                              Microbiology 59.10 (1993): 3187-3196.

Woodward, Andrew M., and Douglas B. Kell. “On the relationship                       between the nonlinear dielectric properties and respiratory                       activity of the obligately aerobic bacterium Micrococcus luteus.”                Journal of Electroanalytical Chemistry and Interfacial                                       Electrochemistry 321.3 (1991): 423-439.

Microbes in Phones in the News

Side note: (They’re on the phones not in them, I just wanted consistency in my titles).

Article:  Scientists Discover 3 New Species of Microbes Growing on Mobile Phones

Source:  Press Trust of India March 6th,  2017

Summary: Microbes live pretty easily on phones, and some scientists in India found 2 new bacteria and 1 new fungus species on the phones they sampled. Tips to clean phones without antimicrobials are included in the article, as they hint at a need to avoid creating super-resistant microbes.

Connections: Mobile phones are used by a lot of people and some people from class got their isolate from their phones, so I believed this article would be something cool to write about.

Critical Analysis: The article explains their findings well, and has enough background/follow up material to get it across to all audiences. The information is displayed in a way that makes you feel as though you are reading a government produced guide on washing your hands, but otherwise the article is fine.

Question: Since the scientists did not sample from phones where super-resistant microbes might be I wonder how the phones that might have super-resistant microbes would differ in their microbial community.

Microbes in Vaccines that made it to the “News”

Article:  Measles Vaccine Suspected Of ‘Horrific Rashes, Illnesses’

Source: Helenesco of Vaxxter April 18th, 2017

Summary: Some “parents” on social media have posted complaining that their children had horrid skin rashes, muscle pains, and fever after vaccinating them with a MR vaccine. Since the only information out there was posted on social media with no doctor’s note or anything the ministry that vaccinated  the children is stating that there is not enough evidence to support their claims (Interesting side note, president Trump is apparently attempting to establish a Vaccine Safety Committee).

Connections: We just got done with the topic of vaccination and how some people see it as a harmful process, so I thought this article would fit perfectly.

Critical Analysis: The website this came from boasts to be “The Ultimate Guide to Vaccine News and Anti-Pharma News, and More,” so naturally the information does portray the information in a sort of biased way, but not as much as I suspected it would. The information is portrayed in a much more factual manner than I thought it would be, and for the most part the bias is minor, plus it does a decent job of getting the information across to many types of people. That being said, the information is only semi-credible most of the time and the potential problem is displayed in such a way that it is highly suggested to be the fault of vaccines, so the most you can do is take it with a grain of salt and acknowledge that it could be a problem due to the vaccines, or not.

Question: If the vaccines did give the children all the symptoms they listed, did it come about as a result of an slip-up in vaccine creation, or some other reason?

Microbes in a Giant Worm in the News

Article: Science fiction horror wriggles into reality with discovery of giant sulfur-powered shipworm  

Source: University of Utah Health April 17, 2017

Summary: Scientists went searching for a type of shipworm they had known about, but had no idea where it’s preferred habitat was. After learning it lived in muddy, shallow lagoons, they took one and had a look at it’s biology where they found that the worm mostly uses/exclusively uses microbes that turn hydrogen sulfide into carbon compounds to get its food. The microbes live in the worms gills and provide carbon compounds to the worm.

Connections: The microbes in the worm’s gills perform anoxygenic photosynthesis that benefit the worm and are a key part of the worm’s microbial community much like humans have beneficial microbes that we use in our microbial communities.

Critical Analysis: I thought the article did a fair job of explaining the results of the scientist’s inquiry into this strange worm and had an overall good background to their study. The article did have some problems though; the title misleads readers into thinking the worm itself uses sulfur as a source of energy when it uses the carbon compounds produced from microbes that use the sulfur. The article did explain this later on, and was written in a way most people could understand, so I have no other complaints.

Question: The article mentioned how this 3-5ft worm likely uses only microbes to sustain itself, so I wondered if it would be possible to find a larger  organism that could exclusively use similar microbes to sustain itself like this worm does.

Painting with or without microbes

I believed too much that my microbe was going to make some fantastic colors for my art, but my faith was misplaced and only one of my works came out okay. The whole piece turned out pretty well and the colors are as good as I can ask for from microbes, so I’m happy with it. The EMB plate made my tree base turn slightly purple and the branches a light gray. I chose the colors based on the way a tree looks covered in snow during winter. The plate did not have much room for me to work with, so a tree was the best I could fit in without ruining the work, otherwise I might have made a different picture.

Introductioney Gunk

Hello my name is David Shilha and I need to post something before I sleep. I don’t have and photos of myself on hand and I  don’t wish to take some, so I hope this is good enough for an introductory pic. I’m not a morning person, but I have morning classes all week and get out of class late. As such I love the time that I have outside of class  because it means I can sleep. I don’t have much time for stuff other than class and sleep, but I do enjoy playing games with friends on the weekends. Hopefully this is a decent enough introduction and if not, oh well I’m still going to sleep.