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



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.

Painting With Microbes: Matt Andrews F03 – Exponential Sunrise

Title: Exponential Sunrise

The intention here was to portray a sunrise over water, with the backdrop of the UAF. We live in an exponential world, whether it is as everyday as the light which lets us see, the sounds we hear, the technology which surrounds us, or even the dirt under our fingernails. The world is built on exponential growth and the education we are developing here at the UAF helps us to understand some small part of it.

I had created this scene on sever plates with Micrococcus luteus (for the golden sun and reflection) and Serratia marcescens (for the red water), I was hoping for a bit more color from the Serratia  but I am still happy with the overall effect.

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.

Painting with Microbes

Samantha Smith F01

Just a wink and a nudge to my favorite book “East of Eden” by John Steinbeck. I have a a pretty cross stitch of this at home, which admittedly looks a lot better. Perhaps I will stick to my day job and leave the microbe painting to those more artistic than myself.

I used the Eosin Methylene Blue Agar plate for this painting, hoping to achieve a stark different in coloration from the two sources I chose. The lettering and the vine were done with Escherichia coli.  This bacteria is gram negative so is not inhibited by the eosin or methylene blue of the medium. It also produced a deep black color with a metallic green sheen as it ferments lactose with strongly acidic end products. (The green sheen is actually quite pretty, though you can’t tell from the photo). The filigree and leaves are colonies of  Enterobacter aerogenes  which is also gram negative. It produces a pink color because it does ferment lactose, but the end products of fermentation are much less acidic than that of  E. coli.

I would like to add that I had a lot of fun in this assignment and seeing the variety of agar art from the ASM Agar Art Contests.


New technique provides a better understanding of bacteria evolution


New technique pinpoints milestones in the evolution of bacteria
Results show bacterial genomes provide “shadow history’ of animal evolution.
Jennifer Chu, MIT News Office February 7, 2019


Danielle S. Gruen, J. M. (2019, January). Paleozoic diversification of terrestrial chitin-degrading bacterial lineages. BMC Evolutionary Biology, 19-34. Retrieved from https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-019-1357-8


—  Summary:  Researchers from MIT have established organism relationships between fungi and bacteria by reviewing the gene for chitinase (an enzyme which helps to break down chitin). Their review of the mutations, and similarities across different species has allowed them to create an evolutionary tree which correlates microbial evolution with fungal evolution. They found that approximately 450 to 350 million years ago, diversification of three separate bacterial groups diversified as the result of gene transfer with a chitinase utilizing fungi. Below is the resulting evolutionary tree with the fungi identified by purple lines and bacteria with blue lines.

(Gruen, et al. 2019)

—  Connections:  This connects with: Microbial evolution, metabolism, and diversification.
Chitinase allows these bacteria to metabolize chitin as an energy source. This allowed diversification of microbes into new niches ones chitin became more prolific in the environment. Gene transfer was said to make it difficult to genomically identify or differentiate bacterial strains, but here the gene transfer has allowed a better understanding.

—  Critical analysis: I found this article very interesting because, most evolutionary trees are based on rRNA sequencing (highly conserved due to form/function). The use of chitinase to correlate evolutionary relationships between fungus and bacteria is interesting. Especially since the origin of chitinase was in a Fungi (a microorganism that doesn’t look like a microorganism) and the gene has been horizontally transferred to bacteria.

The story was very well written and after reading the original journal publication, it was factually and accurately written. The author did as great job in conveying the information to the general population without losing the integrity of the research. I appreciate the writing style and how it helps those (like myself) who aren’t as well versed in the scientific nomenclature, to understand the information and findings from the research.


—  Question:  How many other highly conserved coding regions can we isolate and use in this manner? Are enzymes such as chitinase always highly conserved, or is there slight variations in the conformation, allowing it to mutate without ruining the function of the enzyme?

-Samantha Smith

Microbes Can Prevent Potholes…?

Article: “Scientists hope bacteria could be the cure for potholes” by Talia Kirkland


Source:  Fox News

Date Published: Feb. 5, 2019

Summary:   This article/news story explains how bacteria may be an answer to preventing potholes.   Scientists at Drexel University in Philadelphia have found that bacteria (they did not mention a specific species), when mixed with CO2 and calcium, can change the environment around them to self-produce limestone.   When spread out on a road, they can make the road material stronger and more able to withstand damage that would cause potholes.   The technique is not yet being used, but it may be an alternative for better roads in the future.

Connections:    This article relates to what we have been talking about in class because they are introducing CO2 and Ca2+ to the bacteria to (I assume) get them to use a specific metabolic pathway and get the desired product.

Critical Analysis:   I think it is really interesting that it only requires two simple ingredients (CO2 and Ca2+) to get these bacteria to produce limestone.   There may be other underlying factors that contribute to the production of the limestone, but the fact that they figured this out with these simple ingredients that are extremely common is pretty impressive.   The information seemed to be scientifically accurate since they actually interviewed the scientists who did the research; it makes the article a little more credible.   One thing that I found misleading, and a bit frustrating, was that within the article, they kept using the terms pavement and concrete interchangeably, but concrete and asphalt are different materials that are made in different ways.   I don’t know if they actually tested this bacteria mixture on actual roads or not, but I think there would be a difference if they tested them on concrete versus asphalt.   The scientist kept saying “concrete”, which leads me to believe that they experimented with concrete, which is not the same material that roads are usually made out of, as far as I know (I would be surprised if roads in Philadelphia are made out of concrete, although it is possible).   If that is the case, then this mixture may not actually work on pavement (asphalt) to fix potholes, as they are claiming.   It is also possible that they were actually working with pavement and are just using ‘concrete’ incorrectly, which would be confusing to people who know the difference between the two materials!   Other than that, I think the author did a really good job at keeping the information simple enough for any person to understand it.   I think someone who knows nothing about biology would still be able to follow along and understand what they are talking about.

Question:    The scientists say that the bacteria are changing the microenvironment around them to self-produce limestone, which made me wonder- are the bacteria that they are adding the ones who are actually producing the limestone?   If not, then what changes are they making that cause other organisms to produce limestone?

A2: Microbes in the News- Phytoplankton




This article explains that the World’s oceans are going to change color as a result of climate change. Researchers point out that the base of the food chain in the oceans is phytoplankton. With an increase in water temperature, the phytoplankton will die, resulting in an ocean that is not as green (as phytoplankton have green pigment from the chloroplasts). This article also explained that by using the color of the ocean one can deduce the population of phytoplankton, therefore getting more data on how global warming is affecting the world.


We have been learning in class the different properties of microorganisms. Right now we are learning how the metabolism works. By understanding this concept, I can use my knowledge to fully understand how an increase in temperature would affect the microorganism’s ability to acquire food and survive. Furthermore, we have been learning in class how different microorganisms can change the environment that they are in.

Critical Analysis

I found this story interesting because I liked the concept that you could tell the population of an organism, like phytoplankton, by looking at the color of the water. Although, I can see many variables in trying to actually test this idea. There are many things that can change the color of something, especially in the ocean, so I don’t see how they could do this. I think that this article did a fine job of relaying information to the general public so they could understand topics that they might not have any experience dealing with it. On the other hand, that means that this article most likely left out many concepts that the general public wouldn’t understand, but I would find interesting.


What is the main reason why an increase in temperature of a few degrees would kill phytoplankton?


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.