Characterizing and Identifying a Microbe Isolate from a Cheek Sample

Characterizing and Identifying a Microbe Isolate from a Cheek Sample


                      Microbes are everywhere, in fact they are the most abundant life form on earth. Microbes have been around for 3.8 billion years and were the first life forms on our planet. Bacteria, archaea, and eukarya are some examples of microorganisms. Some microbes are very beneficial to humans, as they are used to produce vaccinations, antibiotics, and food. They can also assist in physiological functions of the human body. Some pathogenic microbes can be very harmful and can cause diseases and infections.

The microbe that was investigated in this study was isolated from a cheek sample. Since some of the most common bacteria present in the mouth is streptococcus and staphylococcus I hypothesize that my isolate will be one of these two strains of bacteria. The bacteria was classified as Streptococcus pneumoniae I-G2. According to the CDC this strain is usually found on the skin or in the mouth and can cause infections in young children, senior citizens, and adults with weakened immune systems. Streptococcus sp. can cause sinus and ear infections, which can be treated with antibiotics. However more serious infections can also be caused such as pneumonia and meningitis. A Pneumonia vaccine can prevent these infections.

Just like how microbes are both beneficial and harmful in the surrounding world, they are also beneficial and harmful in people’s mouths. There are 700 known microbe species that live in a person’s mouth and scientist are still finding more (Burton et al. 2011). Microbes vary from surface to surface. The microbes found on the teeth, cheek, and tongue are all different and have their own individual communities. For example biofilms are present on the surface of teeth and can cause cavities and periodontal disease if they are not physically removed. Biofilm can’t be removed chemically, and this is why the brushing of teeth is more effective in preventing cavities than just using mouthwash. However this same biofilm is not present on the surface of the cheek, gums or tongue. (Gurenlian 2007). Microbes in the mouth can be beneficial because they positively affect mouth and gum health by outcompeting other harmful microbes for resources. Microbes can also be problematic because they can cause cavities and serious infections.

The purpose of this research was to characterize and identify a microbe that was isolated from a cheek swab. After isolating the sample to a pure culture a series of tests were run on the isolate to help gather information about it to identify what it was and how it worked. These tests included gram staining, fluid thyioglycollate test, oxidase test, catalase test, API E test, API strep test and DNA sequencing.


         The sample was collected from a cheek with a sterile cotton swab. The sample was then transferred to a tryptic soy agar (TSA) via quadrant streaking and stored at room temperature to grow for 6 days. After 3 days the TSA plate had little to no growth, however on the 5th day the bacteria scattered the plate. A single, medium sized, orange colony on the TSA plate was transferred to a new TSA plate in order to isolate a bacteria. The process of isolating the bacteria was repeated multiple times until the bacteria on the plate was uniform.

Once isolated, to gather more information about the bacteria, it underwent Gram staining. Gram staining reveals information about the bacteria’s cell wall. After going through the Gram staining process, if the bacteria turns dark purple it is Gram positive, if it turns the bacteria a light pink it is Gram negative. Gram positive bacteria have a large peptidoglycan layer and lacks a lipopolysaccharide layer. Gram negative have a thinner peptidoglycan layer and a complicated lipopolysaccharide layer.

The Gram staining information was helpful, however it doesn’t give enough information to positively identify the bacterium and so a series of physiological tests were performed including: a fluid thioglycollate test an oxidase test, a catalase test, and an API 20E test. The fluid thioglycollate test determines whether or not the bacteria is aerobic, anaerobic, or can be facultative and live in both environments. The oxidase test reveals whether or not the bacteria has cytochrome c oxidase. If the test changes color than it is positive, however if there is no color change than it is negative.  Cytochrome c is involved in the electron transport chain in the cells mitochondria. The catalase test shows if the bacteria contains a catalase enzyme. If the enzyme is present in the bacteria the test will yield oxygen bubbles when introduced to hydrogen peroxide. Lastly, the API 20E test will help identify if the bacteria has any pathogens and if so, what kind, through 21 different physiological tests.

While these physiological tests were also helpful in provided valuable information about the bacteria, to be absolutely certain about the identity of the bacteria, a DNA sample was sent to the DNA Core lab to be sequenced using an Illumina Miseq. DNA sequencing identifies what strain of bacteria the isolate is, as well as gives information about the isolate’s genome, how long it is, the nucleotide sequence, as well as information about the genes. An antibiotic resistance test was also carried out through a disk diffusion test. During this test the bacterium was introduced to various antibiotics and the amount of growth was monitored. If the bacterial growth is uninhibited and grows right up to or under the antibiotic disc then it is resistant to the antibiotic, if there is little to no growth near the disc then the bacteria is susceptible to the antibiotic, and if there is a small amount of growth near the disc, then the bacteria is slightly susceptible to the antibiotic.


         The results of the genotypic and phenotypic tests that were performed during the course of this project are what ultimately helped identify the isolated bacteria. The Gram staining procedure revealed that the bacteria was Gram positive, shown in Figure 1. The fluid thioglycollate test showed bacterial growth at the top of the medium, concluding that the isolate is a strict aerobe. The oxidase test showed no color on the test strip and was therefore negative. The catalase test, when the bacteria came in contact with hydrogen peroxide, bubbles were formed indicating a positive test result. When the API 20E physiological tests were run, the results showed no color change, which means that the results were all negative (Figure 2). When the API 20 Strep/Gram + physiological tests were fun there were observed color changes in some wells, meaning that the tests were positive. The positive result for the VP well indicates that the bacteria contains a pyruvate substrate which helps with acetoin production. The positive ESC well means that the bacteria contains esculin which is a glucosidase enzyme. The ADH well also had a positive result, which shows that arginine is present which is involved in arginine dihydrolase. LAC, AMD and TRE also had a positive result, this means that the enzymes lactose, starch and trehalose are both present and are involved in acidification.

The DNA sequencing results provided a large amount of information about the bacteria including the functional genes present and how they function in the cell. The bacterial strain was Streptococcus sp. and three functional genes present were ATP dependent helicase DinG homolog, metalo-hydrolase M6_Spy0554, and phosphate M6_Spy0533.

The first Antibiotic resistance test (Figure 5) showed that the bacteria was either susceptible to the antibiotics tested (Erythromycin, Piperacillin, Oxacillin, Tobramycin, Cefazolin, Cefotaxime, Cefoperazone, and Amikacin) or the bacterium was not properly inoculated on the Mueller-hinton agar plate as there was no bacterial growth after 3 days. The second test (Figure 6) performed with the same antibiotics showed the same results, no growth on either of the plates. This concludes that the bacterium was susceptible to all antibiotics tested.

Figure 1. Results of Gram Staining

Figure 2. Results of API 20 E

Figure 3. Results for API 20 Strep/Gram +


Test Color Substrate Reaction/enzymes Results
VP Pink after 10 min, brown after 24 hours Pyruvate Acetoin production Positive
HIP Chemicals not available to perform this test n/a n/a n/a
ESC Black Esculin Glucosidase Positive
Pyra Clear Pyrrolidonyl-2-naphthylamide Pyrrolidonly arylamidase Negative
αGAL Clear 6-Bromo-2-naphthyl-D-galactopyranoside Galactosidase Negative
βGUR Clear Naphthol AS-BI-D-Glucuronate Glucuronidase Negative
βGAL Clear 2-naphthyl-D-galactopyranoside Galactosidase Negative
PAL Clear 2-naphthyl phosphate Alkaline phosphatase Negative
LAP Chemicals not available to perform this test n/a n/a n/a
ADH Yellow Arginine Arginine dihydrolase Positive
RIB Pink Ribose Acidification Negative
ARA Pink L-Arabinose Acidification Negative
MAN Pink Mannitol Acidification Negative
SOR Pink Sorbitol Acidification Negative
LAC Yellow Lactose Acidification Positive
TRE Yellow Trehalose Acidification Positive
INU Pink Inulin Acidification Negative
RAF Pink Raffinose Acidification Negative
AMD Yellow Starch Acidification Positive
GLYG Pink Glycogen Acidification Negative

Figure 4. Interpretation of API 20 Strep/Gram +

Figure 5. First antibiotic susceptibility tests result after 3 days of incubation at 37áµ’C.

Figure 6. Second antibiotic susceptibility test results after 2 days of incubation at 37áµ’C.



         Each of the results gathered from the various tests that were run during the course of this study, indicate that the bacterial isolate is a Streptococcus sp. The results of these test not only help to identify the isolate but also provide information about the bacterium and how it functions. The fact that the Gram staining showed that the bacteria was Gram positive means that it has a thick peptidoglycan layer in the cell wall. This layer is crucial to the cell because it provides structural support and a protective layer. Characteristics of Gram positive bacteria include not having an outer membrane, lipopolysaccharides and are generally more susceptible to antibiotics.

The fluid thioglycollate test provided information about the ideal environment for the isolate. Since there was growth at the top of the test tube, the bacteria needs an oxic environment to thrive. This test not only shows what the optimal oxygenic environment is for the bacteria, but also shows where the bacterium can’t grow.  This makes sense considering the sample was taken from the inside of a cheek, where oxygen is readily available.

The oxidase test determines if cytochrome c oxidase enzyme is present in the bacteria sample. This enzyme is involved in ATP production in the mitochondria (Ow et al. 2008). Since the oxidase test was negative, because there was no color change, the bacteria does not produce cytochrome c oxidase enzyme. Just because this enzyme isn’t produced doesn’t mean that the cell doesn’t produce ATP since there are multiple systems that produce ATP.

The catalase test is performed to determine if the bacterium produces catalase enzymes. If the bacteria releases oxygen bubbles when it comes into contact with hydrogen peroxide, then the test is positive from the presence of the catalase enzyme. The catalase enzyme is involved in providing the cell with protection against oxidative toxins that your body produces or comes in contact with. One toxin is hydrogen peroxide which is why the bacteria reacts when they are combined turning it into water and oxygen. If this was not present in the bacteria the toxins that it fights against could affect the bacteria’s DNA. This enzyme is predominantly found in mammalian cells it is reasonable that the enzyme is present in the isolate since the sample site was from a person’s cheek (Scibior et al. 2006). You don’t say if your microbe was positive for catalase

The API 20E test is a physiological test that tests 20 different metabolic processes and provide more information about the bacterium. Since the API 20E test is for Gram negative bacteria the results were all negative for the isolate. This is plausible considering that the bacteria was Gram positive. A second API test was done that is limited to Gram positive, Streptococcus strains. The API 20 Strep strip showed positive results for the VP, ESC, ADH, LAC, TRE, and AMD tests. Each of these positive results contributes to understanding how the isolate functions. The positive result for the VP well means that a pyruvate substrate is present that is involved in acetoin production, which is used in the cell to store energy.  The positive ESC result means that esculin produces glucosidase which helps with breaking down carbohydrates. The positive ADH means that arginine dihydrolase is involved in helping the cell generate energy. The positive LAC test shows that a lactose operon helps transport and metabolize lactose inside the cell. The TRE results reveals that trehalose is present and provide storage and protects the cell when in stressful situations such as if the cell experiences a low growth period. The last positive test, AMD determines that the cell is able to process starch by converting it into an acid.

The DNA sequencing process identified the bacteria strain as Streptococcus pneumoniae I-G2.  This result is justifiable considering bacterial strains of Strep are very common in human mouths, Strep is a Gram positive bacteria, and the isolate showed positive results for an API strip that is geared towards Strep bacterial strains. The DNA sequencing test not only provided an identification for the bacterium, but also gave information on the genes that are present in the bacterium. There was an incredibly large amount of genes that are present, some include ATP dependent helicase DinG homolog, metallo-hydrolas M6_Spy0554, and phosphate M6_Spy0533. ATP dependent helicase DinG homolog is involved in DNA repair and replication. Metallo-hydrolase M6_Spy0554 catalyzes metal hydrolysis of substrates. Phosphate M6_Spy0533 is a ribose phosphate. Ribose phosphate generates pyrophosphate that helps with nucleic acid synthesis.

The last test performed on the bacterial isolate investigated potential antibiotic resistance to eight different antibiotics using the Kirby-Bauer disk technique. This test had two trials done with the same eight antibiotic disks and there was no growth of any kind after both tests were performed which means that the Streptococcus sp. is susceptible to all eight of the antibiotics tests. The antibiotics include Erythromycin, Piperacillin, Oxacillin, Tobramycin, Cefazolin, Cefotaxime, Cefoperazone, and Amikacin. This result of extreme susceptibility is reasonable due to the fact Gram positive bacteria are generally more susceptible to antibiotics. These results match data from studies done on the susceptibility of Streptococcus to the same antibiotics. Erythromycin was found to have been 59% susceptible, Piperacillin 98.2%, Oxacillin 87.8%, Cefotaxime 98.6% (Traub et al. 1997). Tobramycin has no effect on Streptococcus sp. so it has a 0% susceptibility (Brogden et al. 1976). One explanation for why there was no growth on the Tobramycin quadrant is that the other effective antibiotics spread into the quadrant, preventing bacterial growth.

The research for this bacterial isolate, with a multitude of tests performed to gain as much information as possible over the course of two months, was successful. Most of these test were crucial in gaining information to aid in identifying the bacterial strain. If this project were to be performed again, one improvement that could be made is to continue culturing the bacteria multiple times until the DNA sequencing indicates that it is a pure sample before doing the physiological tests. This would eliminate any skewed results that may appear from other bacteria that may be present in the sample.




Burton, J.P., P.A. Wescombe, P.A. Cadieux, J.R. Tagg. 2011. Beneficial microbes for the oral cavity: time to harness the oral streptococci? US National Library of Medicine national Institutes of Health 22:93-101.


Ow, Y.P., D.R. Green, Z. Hao, T.W Mak. 2008. Cytochrome c: functions beyond respiration. Nature Reviews Molecular Cell Biology 9:532-542.


Scibior, D., H. Czeczot. 2006. Catalase: structure, properties, functions. Postepy Hig Med Dosw (Online) 60:170-180.


Traub, W.H., B. Leonhard. 1997. Antibiotic Susceptibility of α- and Nonhemolytic Streptococci from Patients and Healthy Adults to 24 Antimicrobial Drugs. Chemotherapy 43:123-131.


Brogden, R.N., R.M. Rinder, P.R. Sawyer, T.M. Speight, G.S. Avery. Tobramycin: a review of its antibacterial and pharmacokinetic properties and therapeutic use. The Journal of Drug Delivery Science and Technology 12: 166-200.


“Travelers’ Health.”  Centers for Disease Control and Prevention. Centers for Disease Control and Prevention, 05 Aug. 2014. Web. 28 Apr. 2017.



Gurenlian, JoAnn R. 2007. The Role of Dental Plaque Biofilm in Oral Health. Journal of Dental Hygiene 81, No. 5.

Art Project-Microbes in the Solar System

For my art project I decided to paint the planets with microbes and talk about if any microbes were found on each planet, what types they would be based on the planets environment and resources available. I decided to do this because the guest lecture on microbes in space was really interesting and I thought that this would be a fun way to learn more.

This link will go to my presentation, below I have attached my notes for each slide.


Generally thermophilic microbes are archaea, the highest temperatures that a microbe can survive is 250 F. Since the surface of Mercury can range anywhere from -250 F to 800 F microbes wouldn’t be able to withstand such extreme temperature.


Scientists believe that there could be life forms in the clouds that surround Venus. The surface is to hot but at higher elevations its possible that temperatures can cool down enough to sustain life. There is evidence to suggests that microbes once existed when Venus first formed and that they adapted to the environment in the clouds over the years. the microbes that would be found are anaerobic lithoautotrophs microbes.


In this class we have learned all about the microbes present on earth. Here are some microbes that we have learned about.


Anaerobic lithoautotrophs, oligotrophs, and thermophiles would all be the types of microbes that could live on Mars. There has been evidence of ice on Mars which means that there could have once been microbes.


No microbes could withstand the extreme temperatures. However if they could the type of microbe that would live in the hydrogen and helium rich environment would most likely be Anaerobic, extremophilic bacteria


Saturn is very similar to Jupiter as far as the environments go, so similar microbes would live there as well.


If the temperatures can be adapted to the resources available could allow numerous microbes to survive. The availability of water and methane really opens up the range of microbes that could survive there.


Neptune has a very similar atmospheric makeup as Uranus. So microbes found on Neptune would be similar to those found on Uranus.

A2: (Post 3) Zika Vaccine Progress


Image result for zika virus

Article:  The first live-attenuated vaccine candidate completely protects against  Zika infections

Source: utmb Health

Date: 4/10/17






This Zika vaccine is still being developed and only a short time after the Zika outbreak a vaccine has been developed that can completely protect against the virus. When tested on rats after only one vaccine dose the rats were completely protected. The vaccine was made from an inactive, weakened strain of the Zika virus. The virus was weakened to the point that the virus is safe to use in a vaccine. It was created by deleting a section of the viruses genome. This method has been successful in developing vaccines for other infections. The advantage of using a live virus is that the vaccine can be effective in one dose and last a lifetime. This can be very beneficial for people in countries where the Zika virus is common.


This article really fits in well with the immunology lecture, our ELISA disease tracking lab and the virus section that we learned about a little earlier in the class. Zika can be transmitted through the transfer of blood and other bodily fluids, in our lab we were able to see how diseases like this travel and spread from person to person, which is why it is so important to have a vaccine.  In the virus section that we covered earlier this year we learned how some, very few, viruses can be beneficial while most others are harmful. This article provides examples for how viruses can be useful and harmful. The virus is harmful because it causes a disease but its also helpful because scientists know how to manipulate it to create a vaccine.

Critical Analysis and Questions

I think that the progress that is being made towards producing a vaccine that can protect against the Zika virus is very important. When a virus like this presents itself, spreads quickly, and has the potential to really harm people it is a scary time especially when not much is known about how the virus works/effects people and no vaccine is available yet. I was really surprised to see that so much progress has been made towards producing a vaccine, while reading this article I wondered how long it would take for the vaccine to complete the testing process and be approved by the FDA, how long does that process generally take?

Microbial Worlds Art Extra Credit

Art Piece #1: Mysterious Underground Collaboration: Mysterious Underground, Mycorrhizae.

Artists: Charlotte Bird and Ree Nancarrow

Charlotte Bird and Ree Nancarrow

What drew me to this work was the fact that there is so much detail which keeps your attention because each time you look at it you notice something new. The purpose of this art was to promote awareness of what was beneath our feet that we can’t see. I love the cross sectional view point that this piece shows and I think that by doing it from that view point and putting most of the focus on whats under the ground as opposed to whats above it, really gets the point across. Even though the piece does focus pretty heavily on the fungi that are underground it also shows some fungi above ground that we are able to see when out in the woods. I think that it was great and really important that Bird consulted with Dr. Laursen to ensure that the art was accurate, that the fungi were placed in the proper environment and that the plants and fungi were interacting in the art as they would in the real world.


Art Piece #2: Toolick Chain of Lakes Collaboration

Artists: Charlotte Bird and Ree Nancarrow Ree Nancarrow and Charlotte Bird

What drew me to this art is the cool colors and its abstract nature, when I saw that the artists for these pieces were the same artists for  Mysterious Underground Collaboration: Mysterious Underground, Mycorrhizae I was surprised because the styles are so different, almost opposite in fact. This piece is based on the article Biogeorgraphy of Bacterioplankton in Lakes and Streams of an Arctic Tundra Catchmen  by Byron C. Crump Ree consulted with Jason Dobkowski to ensure that the art was accurate. The purpose of this piece was to make the microbial world that surrounds us visible. I think that this concept was really well conveyed in this piece because you can really see a flow and connections between the communities but if you look close you can also see that the art is like a collage of different pictures which I think is meant to represent the different microbial communities present.


Art Piece #3: Deceptive Beauty

ARee Nancarrow rtists: Ree Nancarrow and Debbie Clarke Moderow (writer)

I really liked this art work because its a great depiction of what the lakes surrounding Fairbanks can look like in different seasons, I also really like how we can see the methane bubbles spreading everywhere. The purpose of this piece is to show how methane and carbon dioxide have affected the permafrost and release of methane in the northern lakes. This piece has a great connection to what we have learned in class about how the methane bubbles form and the carbon cycle and the activity that we did in class when we had to draw the carbon cycle.

If I were to participate in the Microbial Worlds art show I would most likely do a piece on how oil spills in the ocean can be cleaned up by microbes. I really found the in class lecture on the topic very interesting. I would most likely use blue and black water colors to simulate the spread of oil in the ocean and than use a white crayon to represent the microbes present that pop up in the black oil.


Extra Credit:Dan T. Stinchcomb Seminar

Dan Stinchcomb spoke about mosquito born tropical diseases, more specifically Dengue Fever. Half of the worlds population is at risk of being exposed to Dengue Fever and there has been a rise in reports of Dengue Fever in tropical urban communities. It is also showing up in more northern and southern regions due to global warming.

Stinchcomb next explained how the disease affects people. The first time that a person is infected with Dengue they will become very sick, however if they survive and come into contact again with Dengue than they have no response to it, since they have developed antibodies to fight the familiar virus. The problem is that there is four different types of Dengue viruses and if a person who has been exposed to the first Dengue virus and becomes sick with the second virus than there is a higher change of infection. There is one vaccine that was approved and still many others in the making. The one vaccine that was approved is called CYD vaccine. CYD was made by taking part of the Yellow Fever vaccine and manipulating it to target the Dengue virus. CYD protects against all four of the viruses, which is good, the downside is that it doesn’t protect against each vaccine equally. The next virus is one the Stinchcomb is working on and its called TDV vaccine.  This was made with the Dengue 2 virus and was effective at neutralizing antibodies response and has gone through phase I and II of testing. Phase I tested to ensure that the vaccine was safe, while phase II focused on how the vaccine effected different age groups.

I really enjoyed this seminar, not only because it was interesting to learn about the spread of diseases and how their vaccines are made but also because it brings awareness to these disease that are such a big problem in tropical parts of the world, which is very important. This talk really relates to what we did in Lab 9 for our antibiotic susceptibility testings. The seminar goes into detail about how disease fighting medicines are created, even though one is focusing on viruses while the lab focused on bacteria. One question I did have was with the first vaccine, CYD, if it wasn’t completely effective than why did it get approved for use? Was it just being pushed through because a vaccine is really needed or does the FDA requirements need to be set to a higher standard?

Painting with Microbes Lab Results

Below are the results for my painting with microbes lab. I think that both of them turned out pretty well. I like the pink hue that the MAC medium gives to the painting, however it does look like either the medium or bacteria or a combination of the two causes fringe around the picture. However the TSB plate was very clear in its lines and didn’t have any cloudiness around the bacteria spots. My EMB plate didn’t turn out very well because I didn’t use a high fermenting bacteria on it, so the bacteria blended in with the dark background.

Extra Credit Eric Collins Seminar


Water samples in the Arctic differ based on location. The flow of the water is important because the make up of microorganisms varies based on where the water originally came from. As well as the type of ice that is present in different locations. Water samples that may be taken at the same location also changes over time because the flow of water has changed due to differences in ice/glaciers beings present thousands of years ago which prevent water to flow through the paths that they do now, since the ice has melted, opening up a new path.

Another factor that adds more diversity to the oceans microorganisms is the freshness and salt concentration of the water. In the Bering Straight the water is generally pretty fresh as well as full of nutrients due to the different currents traveling through the Straight. Water with high salt concentrations is denser than fresh water, while warm water is less dense than cold. This causes different layers of water types in the ocean. However, when the deep water mixes with the shallow water it really causes problems for the Arctic because it can cause the ice sheets to melt.

Thoughts, Critical Thinking, Connections, Questions:

I think that the seminar was very interesting and was easy to follow all of the different topics beings discussed due to the visual aids through out the presentation. I thought that the topic was fascinating, thought I have always loved the ocean. However my interest had always been in the warmer climates due to the vibrant colors of the organisms that lived there. I did think that it was interesting to learn about how the salt concentration, currents, origins, and type of ice all have an effect on the Arctic and the wide variety of microorganisms that are present in all of the oceans different environments. I did have a question at the beginning of the seminar, Collins mentioned that there was an expedition that went to the North Pole to collect samples in 2014, and that he didn’t have those available today because he was still processing them. My questions is how long does it typically take to process samples that are collected from these expeditions?


A2: (Post 2) New Microbe Discovered Trapped in Crystals in a Cave in Mexico

Article Title: Weird Life Found Trapped in Giant Underground Crystals

Source: National Geographic

Publish date: February 17, 2017



Summary : New lithotroph microbes have been found in crystals located in a cave in Mexico. These microbes have been dormant for 10,000 to 50,000 years and are still viable. They have been cultured in a lab and are currently being studied. Scientists say that the microbe is a new microbe species, although it is similar to microbes found in caves and around volcanoes.

Connections: The article talks about ow if these microbes could have survived in such harsh conditions, than it is very possible that microbes could survive and be present on other planets with similar harsh conditions. The article also talked about the concern of contamination while finding, extracting, and studying these microbes. Both of these topics were discussed during out guest lecture given by Professor Eric Collins this Friday (3/24/17).

Critical Thinking: Scientific reports  have not yet been published as scientists are still finding new information and learning about the microbe. The biggest question that is being discussed is if it really is possible for microbes to be dormant and viable for 50,000 years, and if so how? Some think that the microbes originated from a water source and made their way into the crystal or that the microbes slow their metabolism while dormant that they don’t need resources to stay alive or that the microbes are feeding on other microbes around them that have died. Since this discovery is so new its hard to be certain about all of the details of these new microbes, so this article covers a large variety of theories as well as possible ways that this discovery may help discoveries in astrobiology.

Question: Since this microbe could possibly live on a different planet with harsh conditions, will NASA begin to look at planets with similar environments for microbes like the one found in the caves? To clarify with this new discovery will NASA start looking for microbes similar to those found int the crystals on other planets with similar environments?

Simon Lax Extra Credit

Simon Lax-Human Microbiome

Kirsten Veech

     This seminar addressed a very interesting topic, Simon Lax studies culture independent microbiology which is where he collects samples from environments sequences and targets 16S markers which determine a large part of diversity in microbes. These studies don’t look at microbes that are grown in labs. Lax’s research was focused on the human microbiome and how a persons microbiome is changed depending on their skin condition, environment and surroundings, and pets. The main questions that Lax was pursuing are; How much did home surface microbes resemble their occupants microbes? How unique microbe communities in individual homes are? What are there major interactions between people and their environment? and How stable are these microbe communities?

     These questions were answered by Lax conducting a study on 7 families who took samples from their skin, home surfaces, and pets every 1-2 days from 4-6 weeks. Lax found that surfaces in home do resemble their occupants quite a bit, more specifically he found that the occupants feet resembled the floors of the house while the occupants hands more closely resembled the counter and doorknob surfaces. This finding makes sense considering the transfer of microbes from hands to doors and feet to floors. By using beta diversity he also found that there was not a unique environment in different homes, there was a well mixed environment in each home. He found that there was a larger variety in homes with multiple occupants and pets vs a single occupant home. So to be clear the microbes found in homes were similar across the board. Stability of microbe communities was determined by comparing surface samples from day to day. Lax found that peoples hands had a low stability possibly due to the large amount of interaction with different environments through out the day while the floors had high stability.

     A really interesting point that Lax brought to our attention was that when a person leaves the home environment for a little while their “microbial signature” as he called it, will go away. This makes sense because that person is not coming in contact with these surfaces and keeping their microbial signature present, however I would have thought that their microbes that they brought to the house would have stayed present because they were in environments that they could live in so what would cause them to leave that environment if they have already successfully habituated there? This really shows what we learned in class that microbes are everywhere, and its super interesting that they are, in a way organized in their location around us. Its so cool to think that a single celled organism can be “organized” (using this term loosely because they don’t organize themselves, but certain microbes are more common in certain places).

A2: Why are there glowing beaches around the world?

Title: 6 Incredible places where the oceans glow

Source: Mother Nature Network (

Article date: July 14, 2016

Summary: This article talks about the glowing beaches that have been seen around the world and the science behind why they are glowing. There are phytoplankton in the sea that respond to electrical signals by emitting a blue glow when moved or disturbed making the beach look like its filled with stars.

Connections: In class we have discussed that microbes are everywhere, that they can have good (medications) and bad (diseases) effects and that they are beautiful. Well this article certainly focuses on the beauty that microbes are responsible for. To more specifically name a topic that has been covered in class, this article really relates to the physiology of a cell. The physiological reason for why the phytoplankton glow is because there is a reaction called luciferin-luciferase and it occurs in organelles called scintillen. Thousands of these organelles are what causes the bioluminescence. Phytoplankton without scintillen do not have the bioluminescent effect.

Critical analysis: This article was interesting and caught my attention because there were these beautiful beaches that had blue waves that seemed to be glowing and I was curious as to why/what made this happen. I learned that the scientific name for the specific type of phytoplanktin is Noctiluca scintillan. Noctiluca scintillan is responsible for what makes the beaches look like they are glowing. Noctiluca scintillan is a single celled protist who’s cytoplasm glows when disturbed. As far as scientific accuracy goes there has been some disagreement as to whether or not the glowing organism is phytoplankton or ostarcod crustaceans. The Huffington Post wrote an article that quoted a Cornell professor who argued that the organisms are actually ostarcod crustaceans but are commonly mistaken for phytoplankton. Other articles that I found credited phytoplankton for the glow in the waves. So it seems that article is scientifically accurate, there is just some argument between scientists as to what organism is actually responsible for the glow.

Question: While reading this article a question popped into my mind. Why do these organisms only sometimes show themselves? What makes them sometimes glow and sometimes not and what is the determining factor there? I know that they probably are only seen in certain places (that all seem to have warm climates) because that is most likely their ideal environment. But the article says that some  times they show up while other times they don’t. Which makes me wonder what causes this to happen.