Micrococcus Luteus


Microbes are too small to be seen by the naked eye; they can survive in conditions that many would think are unlivable like the anaerobic environment in the rumen of cows, hot springs, and cold Antarctic waters (What are microbes, 2010). Millions of microbes live both on and in the human body and can both make help us survive or make us sick, less than 1% of bacteria cause disease (What are microbes, 2010).

The nasal cavity microbiome primarily consists of the phyla Actinobacteria, Firmicutes and Proteobacteria (Bassis et al. 2014).  The microbiome of the nasal cavity can also change in response to environmental factors such as geographic location, and hygiene (Rawis et al. 2019).

Micrococcus luteus is found in lots of places including skin, soil, dust, water, air, mouth, mucosae, oropharynx, and upper respiratory tract of humans (Wikipedia, Micrococcus luteus, 2019). It is a gram positive, coccus shaped microbe, and contains catalase. This microbe forms large, round colonies. It can be easily be mistaken for staphylococci, as they are very similar morphologically and physiologically (Wikipedia, Staphlyococcus Aureus).

My goal in this experiment was to isolate, characterize and identify a bacterial colony that arose from a sample taken from my roommate’s nose. I hypothesized that it would be a bacteria commonly found in the nasal cavities and likely from the aforementioned phyla, so it would likely do best living in an aerobic, humid, and warm environment.


I chose to sample bacteria from inside my roommate’s nose. To sample, I used sterile cotton swabs and streaked them on TSA plates. I kept the plate at room temperature for 7 days, and then selected a colony to purify using the pure culture streak plate method. I repeated this process three more times to further purify the colony. Once the culture was deemed pure enough, I inoculated a slant tube.

I performed many tests to find out the colony morphology and physiology. In order to determine physiological characteristics of the culture such as cell shape, arrangement, and whether it was gram positive or negative, which helps determine the cell wall type of the microbe, I performed a gram stain. I used an oxidase test strip and water to determine if cytochrome C oxidase was present, and performed a catalase test to determine if catalase was present. I also did a fluid thioglycolate test to determine the bacteria’s oxygen class. I grew my bacteria on an Eosin Methylene Blue (EMB) plate to see if it could ferment lactose and if it could grow with methylene blue which selects for gram negative bacteria. I also grew it in a MacConkey (MAC) plate to see if it could ferment lactose and if it could grow with both crystal violet and bile salts to further confirm if it was gram negative or positive. I used an API Strep test to determine more of the sugars the bacteria could ferment.

I grew my isolated in Tryptic Soy Broth (TSB) for a week to prepare for DNA extraction. I extracted the DNA using the PowerSoil DNA kit (manufactured by Qiagen) following manufacturer instructions. The sample was then sequenced using the Illumina MiSeq technology in UAF’s DNA Core Lab. I used the PATRIC software to perform a metagenome binning and to assign a taxonomy to the bacteria.


The colony took 16 days to be purified. The gram stain of this microbe showed that it is gram positive because it stained purple. This microbe is coccus shaped and forms in tetrads. The colony forms as a yellow, shiny round blob. The catalase and the oxidase tests came up negative, because the catalase test did not form bubbles, and the oxidase test did not see a color change. The oxidase test tests to see if the microbe contains cytochrome c oxidase. The catalase test tests to see if the microbe contains catalase. The fluid thioglycallate test showed that the bacteria was an obligate aerobe because the growth was concentrated at the top of the tube in the pink region. The MacConkey agar showed very little growth, and did not have a change in color, indicating that the microbe was gram positive and not a fermenter. The EMB agar showed no growth or change in color, also indicating the microbe was gram positive and a non-fermenter.

The API 20 Strep test I used came up with no conclusive results. This test had VP, HIP, ESC, PYRA, aGAL, bGUR, bGAL, PAL, LAP, ADH, RIB, ARA, MAN, SOR, LAC, TRE, INU, RAF, AMD, and GLYG tests. The PYRA, PAL, LAP, RIB, ARA, MAN, and TRE tests came up as positive.

The taxonomic assignment of this microbe was micrococcus luteus because it was the only bin that PATRIC gave. It had 27,372 contigs in assembly. It has multiple antibiotic resistance genes including dihydropteroate synthase, glycerophosphoryl diester phosphodiesterase, and SSU ribosomal proteins.

Figure 1. Krona chart of microbe shows bacterial classes thought to be present in the sample.

Figure 2. Kaiju webserver metagenome binning analysis chart. It shows that the sample contains bacteria from the Terrabacteria group. It is mostly Actinobacteria, but some Proteobacteria and Firmicules are in the sample as well.

The kaiju metagenome binning shows that the microbe sample is not completely pure (Figure 2). It shows that it is mostly Actinobacteria, with some firmicules ,and proteobacteria mixed in (Figure 2). This matches up with the PATRIC metagenome binning which also showed some impurities (Figure 1).



As the microbe is gram positive this means that it has a large peptidoglycan layer and lacks a lipopolysaccharide layer. The MacConkey agar is selective for gram-negative which is why my microbe didn’t show much growth on it, and because it didn’t change colors it means it didn’t ferment the lactose. The EMB plate is also selective for gram-negative bacteria which is probably why the bacteria didn’t grow on it. The oxygen class of the microbe, obligate aerobe, matches up with the predictions I had made about it because the bacteria was originally sourced in a nostril. Wikipedia also says that Micrococcus luteus is an obligate aerobe, backing up what my results show (2019).

The oxidase test results suggest that the microbe does not contain oxidase, despite what the metagenome binning test showed. The catalase test also indicated that the microbe does not have catalase, despite the metagenomic binning test suggesting it. These discrepancies could be due to human error, unpure culture, or an old agar plate. The API test strips’ lack of results suggests that the I used   the wrong test strip, I probably needed to use the Staph test instead of the Strep test, because the Strep test is for when Catalase is absent, but there could have been catalase present. The conflicting results of the metagenome binning and the catalase test influenced this mistake. I think based on all this information, that my microbe is in fact micrococcus luteus as suggested by the PATRIC metagenome binning test, and the krona (Figure 1).

In conclusion, some of my results were inconclusive and conflicting. This is likely either a cause of human error, unpure cultures, or not using agar plates that are fresh enough for the test. I think that this culture was mostly Micrococcus luteus based on the Kaiju and metagenome binning results. The oxygen class and the gram positiveness of the microbe also matches up with that of Micrococcus luteus. In future works with this microbe, I probably would want to purify the culture more and redo the tests.



Bassis CM, AL Tang, VB Young, and MA Pynnonen (2014). The nasal cavity microbiota of healthy adults. Microbiome 2(27).

Rawis M, and AK Ellis (2019). The microbiome of the nose. Annals of Allergy, Asthma and Immunology 122(1):17-24.

(2010) What are microbes? Institute for Quality and Efficiency in Health Care.

Wikipedia contributors. (2019, March 14). Micrococcus luteus. In  Wikipedia, The Free Encyclopedia. Retrieved 06:20, April 16, 2019, from  https://en.wikipedia.org/w/index.php?title=Micrococcus_luteus&oldid=887698104


Wikipedia contributors. (2019, April 4). Staphylococcus aureus. In  Wikipedia, The Free Encyclopedia. Retrieved 22:17, April 16, 2019, from  https://en.wikipedia.org/w/index.php?title=Staphylococcus_aureus&oldid=890960280



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?

“Harry Potter and the Lesson in Latin”

Savanna Ratky:

I created a short comic using crayons and pens to draw on paper. I made it Harry Potter themed, as that is a series that I enjoy, and that I thought most readers would relate to. I specifically made this about the iconic scene where Hermione, Ron, and Harry are trying out a new spell and Ron mispronounces it as LeviosA. Hermione then corrects him by saying “it’s LeviOsa not LeviosA’. The concept I chose to make the work about was specifically the use of “bacterium’ and “bacteria’, which are commonly missued by people. Bacterium is the singular version of bacteria.

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?

Savanna’s Flower

Savanna Ratky F03

My artistic intent for this project was to make a flower out of microbes, I put micrococcus luteus in the center with the intent that it would turn yellow (it didn’t really), I put serratia marcescens for the petals because its supposed to be red/pink (also didn’t become pink), and I put citrobacter freundii for the little swirls around the flower with the intent that they would be white. This was on a TSA plate because the list of microbes with their colors are on TSA plates, so I chose this because I thought the colors would change to the colors on the list, the color of the plate didn’t really change and I didn’t expect it to.

A3: Epithet Epitaphs

Walborg Thorsell  (1919-2016) was a Swedish veterinary scientist who studied mosquitos and mosquito repellents because there was talk about malaria infected mosquitoes being used as biological warfare. Thorsell found that diethylamide was more effective than the common repellent deet.


Thorsellia bacteria are named after Thorsell because they are found in mosquito species that are common vectors for malaria in Africa, Asia, and South America. Thorsellia is founded in waters were mosquitoes breed, and can live in alkaline conditions, and grow faster in blood culture. Alkaline conditions are found in mosquito larvae. Thorsellia has also been found in mosquitos that are carriers of West Nile virus and encephalitis.





A2: Microbes in the News: 1

A Silver Bullet Against the Brain-Eating Amoeba?

-New York Times

-January 14, 2019

I found an interesting article about a new way to stop  Naegleria fowleri, a brain eating amoeba found in freshwater ponds in the US. They are using silver particles covered in anti-seizure medication, which can kill the amoeba.

This article intrigued me because I haven’t heard of anyone having brain eaten amoeba in the United States, I didn’t know that there were any diseases like this occurring here. This article appears to be scientifically accurate. I think this article did a good job at communicating a new discovery by mixing quotes and scientific information.

This article mentions using crickets, mice and cockroaches as animal models for future testing. My question is why are they using these bugs to carry out these experiments rather than a model species?