Lab Report for the Term Project

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Physiological and Genetic Identification of Streptococcus salivarius Isolated from the Oral Cavity

Introduction

This world would not be the same without microorganisms which play a prominent role in it. Bacteria are extremely diverse, abundant, and have the ability to occupy almost each niche of the world’s habitat, choosing it according to each bacteria’s nutritional and energy needs. The human oral cavity is not the exception.

With the above background, the oral microbiota was chosen for the following experiment. The oral cavity has all possible favorable conditions for microorganisms such as temperature, pH, humidity, nutrients, and oxygen if needed. In the oral cavity, bacteria can reside on the mucous of the buccal vestibule, at the tongue dorsum, periodontal pockets, tonsils, and teeth surface. The most predominant genera for oral microbiota include but not limited to Streptococcus, Veilonella, Lactobacillus, Actinomyces, Haemophilus, and Neisseria (Belstrom et al., 2016; Lif Holgerson et al., 2015).

The objectives for this study were to isolate, characterize, and identify a bacterium from the oral cavity. The sample was obtained by placing a cotton swab in the oral cavity of a human. The pure culture was isolated through a series of streaking methods. To obtain taxonomic characteristic for a microbial isolate, a series of physiological and genetic tests were conducted followed by series of antibiotic resistance tests. It was determined that the microbial isolate was the bacterium Streptococcus salivarius.

Methods

To start the experiment, I obtained two samples: one from the oral cavity of a human and the other one from the ear of my cat Tima. I moistened a sterile cotton swab with sterile water provided for each sample collection, swiped inside the cat’s ear and inside the oral cavity of a human, and inoculated two samples to a tryptic soy agar (TSA) plate and a Sabouraud’s agar (SA) plate with it. I put a Parafilm strip around each media plate and kept them at room temperature. After forty-eight hours, all media plates were placed in my boiler room with a bit higher temperature to encourage bacterial growth. I allowed cultures to grow and form colonies.

Once bacterial colonization visibly occurred, I chose a bacterial colony, reinoculated it to a new TSA plate using a streak plate method, and kept the media plate in the incubator at 370C to grow. I repeated the streaking plate method and grew the bacterial culture two more times with an interval of forty-eight to seventy-two hours to isolate a truly pure culture. I took notes on the isolate colonies color, size, shape, elevation, and margins.

Next, I determined if my bacterial isolate was Gram-positive or Gram-negative and used the Gram staining techniques for this process (Lab 4 protocol). Also, I inoculated a tryptic soy broth (TSB) with my bacterial isolate and a slant, for genomic DNA extraction and storage in the fridge, respectively.

To characterize physiological traits of my bacterial isolate and determine its possible identification, I used a series tests including:  fluid thioglycolate, oxidase, catalase, and an API20 E test kit designed for enteric, Gram-negative bacteria. (Lab 6 protocol).

The genomic DNA extraction was performed using the PowerSoil DNA isolation protocol (Lab 5 protocol). I harvested cells from my liquid culture of bacterial isolate in TSB and placed them in a PowerBead tube; then, I lysed all bacterial cells with sodium dodecyl sulfate (SDS), centrifuged the mixture at 10,000 on the microfuge and obtained a supernatant. Then, the genomic DNA was purified from proteins, inhibitors, and enzymes by bounding to a “spin filter’ and washed. Finally, I eluted the clean DNA and it was stored at -200C. The genome of my DNA sample was sequenced by the UAF Arctic Biology DNA Core Lab technician via an Illumina MiSeq.

Using the cloud-based software BaseSpace and the applications provided: SPAdes Genome Assembler, Prokka Genome Annotation, and Kraken Metagenomics, I was able to assemble all DNA sequences obtained from Illumina MiSeq sequencing into a bacterial genome, annotate the genes and determine several functional genes, and give a taxonomic assignment to my bacterial isolate, respectively.

And, the bacterial isolate’s susceptibility and resistance to a variety of antibiotics were both tested following the protocol for the Lab 9.

Results

After inoculating complex TSA and selective SA media with a sample form oral cavity, the bacterial growth occurred in about seventy-two hours at 370C on the TSA plate but not on a SA plate. The sample from cat’s ear did not appear to grow on any of two media. From oral cavity, pure bacterial culture for the term project was obtained within approximately fourteen days; four TSA media were used for this purpose. This bacterial culture grew very slow. After growth on TSA, the microorganism formed glossy, white (almost translucent) colonies. Bacterial colonies were 0.8-1.0 mm in diameter, had a round shape, smooth edges, and slightly elevated above the media (Photograph 1).

The Gram staining technique with subsequent sample microscopy revealed that the bacterial isolate was Gram-positive spherical cocci. The bacterial cells were mostly dissociated, some cells arranged in small clusters, and other bacterial cells occurred in short chains.

Photograph 1. Streptococcus salivarius colonies on TSA

The bacterial pure culture appeared to be an aerotolerant anaerobe as it grew equally well throughout the fluid thioglycollate test tube (Photograph 2). Oxidase, catalase, and API 20E test results were all negative.

Photograph 2. Thioglycollate test results

The identification of the bacterial isolate was completed via genomic DNA extraction, followed by genomic sequencing, assembling, and annotation. One hundred and eighty-three contigs were assembled, and about two thousand coding regions were found. S. salivarius species name was assigned to my bacterial isolate with the confidence of 97.06% on the species level (Photograph 3).

Figure 3. Classification results by taxonomic level

S. salivarius culture appeared to be susceptible to Tetracycline, Vancomycin, and Gentamycin. The bacterial strain was intermediate to Cefoperazone, Amikacin, Piperacillin, and Cefotaxime. S. salivarius strain showed resistance to trimethoprim (Photograph 4).

Photograph 4 Streptococcus salivarius appeared to be resistant to Trimethoprim

Discussion

Due to difficulties in obtaining results from the API 20E test, the genotypic test was primarily used in the identification of the bacterial isolate for the term project. The DNA sequence was run through the cloud-based software BaseSpace and received the taxonomic assignment of Streptococcus salivarius species in 97.06% reads. The salivarius group of commensal organisms contains three genetically similar species, S. salivarius, S. vestibularis, and S. thermophilus, which are predominant species associated with oral health (Belstrom et al, 2016; Delorme et al., 2014).

The genotypic test results explained the difficulties with the API 20E physiological test. S. salivarius is Gram-positive and the test named above, was created for enteric Gram-negative bacteria, so the growth of Gram-positive bacteria would not occur. If I could run any additional physiological tests, I would use an API Strep test kit to elucidate specific metabolic traits exhibited by my isolate.

“Virtually all’ Streptococcus strains are facultative anaerobes, and some may require additional CO2 for growth; they are also catalase- and oxidase-negative (Boone, 2001-2012). Bacterial strains belonging to the S. salivarius species though, can be grown on suitable media in the presence of oxygen at temperatures up to 45oC (Boone, 2001-2012). This information explained the very slow growth of the bacterial isolate on TSA and in room temperature. Bacterial culture growth was somewhat increased when in the incubator, but was enhanced further, when grown in liquid media such as in the TSB. S. salivarius is tolerant to oxygen but preference for hypoxic conditions explained the results observed in this study for the liquid thioglycollate test.

The bacterial isolate was found to be susceptible and intermediate to most antibiotics tested in the Lab. However, the absence of an inhibition zone around Trimethoprim suggests that the bacterial isolate was resistant to this antibiotic. In their study, Barbour and Philip (2014) tested the S. salivarius isolate and found the strain to be resistant to Gentamicin (Barbour & Philip, 2014). In general, this bacterial strain of S. salivarius was sensitive to antibiotics that controlled upper respiratory tract infections (Barbour & Philip, 2014).

  1. S. salivarius is mainly encountered in the mouths of humans particularly on the tongue and in the saliva, and “can display a probiotic potential’, by decreasing “oral malodor’, and may reduce inflammation (Boone, 2001-2012; Roger et al., 2011). In order to maintain a competitive advantage in the oral microbiome, S. salivarius produces a bacteriocin-like substance called lantibiotic “with therapeutic potential in treating infectious diseases’ caused by other pathogenic microbes commonly found in the mouth (Barbour & Philip, 2014).

In conclusion, this term project was successful and revealed the presence of S. salivarius strains from the human oral cavity. Genome sequencing was integral in obtaining the taxonomic ID and phenotypic tests were only partially successful as the API 20E test strip was not ideal for use with this microbe, and certain environmental conditions such as increased amount of CO2 and temperature (45oC) were unavailable. There is still not enough data on lantibiotic-producing strains of S. salivarius. Further research in this direction might highlight some aspects in the maintaining of human mouths at healthy levels.

 

 

 

 

 

 

 

References

Barbour, A., Philip, K., & Muniandy, S. (2013). Enhanced Production, Purification, Characterization and Mechanism of Action of Salivaricin 9 Lantibiotic Produced by Streptococcus salivarius NU10. Plos ONE, 8(10), 1.   Retrieved from https://web.b.ebscohost.com.proxy.library.uaf.edu/ehost/pdfviewer/pdfviewer?vid=5&sid=d0127794-9f22-4a10-9b4f-15447fd3a0c4%40sessionmgr102

Barbour, A., & Philip, K. (2014). Variable Characteristics of Bacteriocin-Producing Streptococcus salivarius Strains Isolated from Malaysian Subjects.  Plos ONE,  9(6), 1-16. Retrieved from https://web.b.ebscohost.com.proxy.library.uaf.edu/ehost/pdfviewer/pdfviewer?vid=8&sid=d0127794-9f22-4a10-9b4f-15447fd3a0c4%40sessionmgr102

Belstrom, D., Holmstrup, P., Bardow, A., Kokaras, A., Fiehn, N., & Paster, B. J. (2016). Temporal Stability of the Salivary Microbiota in Oral Health. Plos ONE, 11(1), 1-9. Retrieved from https://web.b.ebscohost.com.proxy.library.uaf.edu/ehost/pdfviewer/pdfviewer?sid=909c9530-2cf2-4423-8d29-8b78abde18da%40sessionmgr104&vid=2&hid=116

Boone, David R. (2001-2012). Bergey’s manual of systematic bacteriology / George M. Garrity, editor-in-chief. New-York: Springer

Delorme, C., Abraham, A., Renault, P., & Guédon, E. (2015). Genomics of Streptococcus salivarius, a major human commensal. Infection, Genetics & Evolution, 33, 381-392. Retrieved from https://resolver.ebscohost.com.proxy.library.uaf.edu/openurl?sid=EBSCO%3aaph&genre=article&issn=15671348&ISBN=&volume=33&issue=&date=20150701&spage=381&pages=381-392&title=Infection%2c+Genetics+&atitle=Genomics+of+Streptococcus+salivarius%2c+a+major+human+commensal.&aulast=Delorme%2c+Christine&id=DOI%3a10.1016%2fj.meegid.2014.10.001&site=ftf-live

Lif Holgerson, P., Öhman, C., Rönnlund, A., & Johansson, I. (2015). Maturation of Oral Microbiota in Children with or without Dental Caries.  Plos ONE,  10(5), 1-20. Retrieved from https://web.b.ebscohost.com.proxy.library.uaf.edu/ehost/pdfviewer/pdfviewer?sid=61460fa1-2a9f-4c88-b707-34db0fd4fa02%40sessionmgr102&vid=2&hid=116

Roger, P., Delettre, J., Bouix, M., & Béal, C. (2011). Characterization of Streptococcus salivarius growth and maintenance in artificial saliva. Journal of Applied Microbiology, 111(3), 631-641. Retrieved from https://web.b.ebscohost.com.proxy.library.uaf.edu/ehost/pdfviewer/pdfviewer?vid=13&sid=d0127794-9f22-4a10-9b4f-15447fd3a0c4%40sessionmgr102

“A Hand to Life”

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In my project called “A Hand to Life’, I wanted to express the importance of Life and Balance in it.

The diversity of species on Earth is balanced so far. Each finger on the Hand represents a “branch’ (a.k.a., domain) from well-known “Phylogenetic Tree’ theory. You can see Bacteria, Archaea, Eukarya, viruses (a.k.a., NCLDV) blended together, as we know them.

With the recent increased interest to Space exploration, we must get ready to find something “there’ or never find anything. That’s why there is a “Question mark’ on the “thumb’. We don’t know what is “there’. Is it the Life that we know or is it something that we are not ready to explain? In any way, the Hand represent the readiness to accept whatever is there to our big Family that we want to keep in Peace. But, we don’t want to lose the Balance either…

Bacteriophages, Natural Drugs to Combat Superbugs

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Title: Bacteriophages, Natural Drugs to Combat Superbugs

Source: ScienceDaily (the source for latest research news)

Date: April 18th, 2017

The link: https://www.sciencedaily.com/releases/2017/04/170418160032.htm

Summary: In this article, the researchers are trying to use bacteriophages to help fight the bacteria resistant to antibiotic treatment. As bacteria are becoming more resistant to antibiotics, it raises the potential problem of running out of possible antibiotics to use in severe cases. It takes a long time to get a new product to the market. We lack this time. That’s why the researches need new ideas. One of them was to try and use bacteriophage against bacteria inside the host. So far, there are twelve bacterial strains that resistant to antibiotics, collected in the lab. None of the available phages can kill the antibiotic-resistant E. coli, the sequence type 131. The researches acquired bacteriophages from feces of birds and dogs. The researchers believe that those species can carry phages for resistant bacteria. In the lab, mice models are used to mimic how cancer patients develop life-threatening infections as the disease progresses. When the immune system is compromised, and cannot detect antibiotic-resistant bacteria, it is believed that phages can step in and deal with them. The question to further research here, is the phage specificity to certain bacteria only and the host’s immune system sometimes can neutralize phage’s activity.

Connections: The material about bacteriophages and their lifestyles, lytic (virulent) and lysogenic (temperate) replication cycles was covered in the lectures. It is nice to read in depth about the material that you already learned and know.

Critical Analysis: I’ve chose the article because it was interesting to find out how this research was implemented. The article is well-written and provide good background information, together with present experiments with ideas for the future research. Of course, some time is needed to put it all together and conduct more experiments until the phage will be able to work inside the immunocompromised host.

Question: What are your thoughts on “phage’ treatment? What do you think will happen to the immunocompromised host when the phage will destroy bacteria, and all toxins would be released? For some reason, I thought about this right after reading this material.

Researchers Create Self-Sustaining Bacteria-Fueled Power Cell

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Title: Researchers Create Self-Sustaining Bacteria-Fueled Power Cell

Source: Phys.org

Date: March 22nd, 2017

The link: https://m.phys.org/news/2017-03-self-sustaining-bacteria-fueled-power-cell.html

Summary: The researches in Binghampton University, NY are working on microbial fuel cells project. The latest results demonstrated the ability of two synergistic microorganisms to coexists in closed environment (one-fifth of a teaspoon) as symbiotes. This co-culture of heterotrophic and photosynthetic bacteria together can generate the power, – an electrical current of 8 microamps per square centimeter for thirteen days. Phototropic bacteria use the light, CO2, and water to exist; and, heterotrophic bacteria can live on provided organic matter or eventually start using the resource from phototropic bacteria, so the closed self-sustained system will occur. This project has a great potential in the future. The challenges are in balancing both microorganisms’ growth in the closed environment and questioning if additional maintenance will be needed. Therefore, more time for further experiments required.

Connections: We have spent enough time in the class covering microbial metabolism and physiology, and calculating amount of energy while comparing different sources of it. That was a good repetition.

Critical Analysis: The concept used in this research is promising because the system proved to work and sustain itself for thirteen days. Of course, the further research and data analysis is required which is understandable. I didn’t know the site “Phys.org’ before but there were several good articles to read. This article was written for the Journal of Power Sources and will appear in print on April 30th, 2017.

Question: Do you know any other examples of symbiotic microorganisms used in other research projects?

Title: Five HIV Patients Left “Virus-Free’ with no Need for Daily Drugs in Early Vaccine Trials

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Title: Five HIV Patients Left “Virus-Free’ with no Need for Daily Drugs in Early Vaccine Trials

Source: “Independent’ Magazine, UK

Date: February 23rd, 2017

The link: https://www.independent.co.uk/life-style/health-and-families/health-news/hiv-aids-vaccine-therapy-trials-no-daily-drugs-art-irsicaixa-barcelona-beatriz-mothe-a7596521.html

Summary: Researchers conducted a clinical trial over three years in Barcelona, Spain. Two therapeutic HIV vaccines have been used in combination with the drug that was usually used in the treatment of cancer. Within twenty-five participants, the virus was undetectable in five volunteers as the immune system kicked back in and stopped the virus spreading in the body. One of the volunteers did not have to take antiretroviral medications for a period over seven months. The HIV affected more than 18 million people in the world. The single treatment that was used so far, is the antiretroviral drugs which can slow down the infection progression, but these drugs must be taken on daily basis. The vaccines used in the trial, were therapeutic and could potentially control the virus without daily medication intake.

Connections: As we spoke in the class, we can acquire artificial immunity via active immunization (vaccination with controlled dose of harmless antigen) and passive immunization (injection of antiserum containing antibodies). Those are preventative measures and must be performed prior the diseases affecting the organism.

Critical Analysis: The therapeutic vaccines used for treatment not prevention. We didn’t cover this material in the class, so I’ve looked on the Internet. The purpose of therapeutic vaccines is to help people, already infected with HIV, to maintain lower viral load that supposedly, do not require the daily dose of antiretroviral drugs. Therapeutic vaccines are theoretically possible but still undergo developmental stages. The authors used “Aids’ instead of official “AIDS’ in the article which caused a lot of comment from people to use the right abbreviations. I couldn’t find a peer-reviewed article to confirm those “therapeutic vaccine’, thus, will read that kind of information with caution.

Question: Did anyone know about “therapeutic vaccines’? I wonder what is the content of them and what is causing to maintain lower viral loads?

Painting with Microbes

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For the project “Painting with Microbes’, I chose to tell about cold winters in Fairbanks. The time when people see a lot of Northern Lights, try to stay warm, and dream about spring to arrive faster. That’s why the following “paintings’ were named “The warming fire’, “Aurora Borealis’, and “The Chamomile’, respectively.

The TSA plate with “The Chamomile’ on it was inoculated with K. rhizophila, B. cereus, and P. aeroginoza to produce yellow, off-white, and clear-green colors, respectively. The TSA medium is just complex, not selective. So, the “colors” from bacteria turned out just right.

The EMB medium is both selective and differential. The EMB is selective medium for Gram-negative bacteria and the plate was inoculated with S. marcescens for “The Warming Fire’ project. This microorganism is Gram-negative and produce less acid which turn the media color pink to “reddish”.

On the selective and differential MAC media, the “yellow’ stars are “made of’ K.rhizophila,  a Gram-negative microorganism.

Developing vaccines for mosquito-borne viral diseases by Dan Stinchcomb

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Dan Stinchcomb recently joined the Infectious Disease Research Institution that employs over a hundred of scientists (39 of them have PhD per Dan). Dan launched at least three different projects there already: vaccine against tuberculosis are being tested in phase 2 (checking if the reoccurrence of the disease will be prevented); working on West Nile vaccine; and developing RNA vaccines. West Nile virus was first discovered in 1937. Birds are the reservoir for this virus which can be transmitted to humans through a mosquito bite. In 2002, the West Nile disease was first registered on the territory of the United States in NY and spread with birds throughout the country in 2003-2004 with a peak in 2006 and 2012-2013, so the U.S. needs a vaccine against this disease.

Dan lectured the audience on Dengue fever, Chikungunya disease, Zika virus, and introduced to RNA vaccines potential.

Dengue fever affects about 390 million people per year. It is a mosquito-borne infection and cause by the virus that has 4 strains (DENV-1, DENV-2, DENV-3, DENV-4). This disease mostly occurs in urban communities in tropical climate. The challenge in creating a vaccine against this disease is in that this vaccine must protect against all four types of virus, otherwise, it will increase the chance of the individual to get the Dengue fever via other virus strains and the disease will be severe with a lot of complications. Currently, there is one vaccine Yellow Fever/Dengue chimera by NiAiD, Takeda in phase 3 testing. This vaccine protects equally against all four virus types but still a bit low on DENV-2; the vaccine provides a good protection to individual that was exposed to Dengue fever in the past. The vaccine is not so effective in individual that was never exposed to the disease; the danger is in getting secondary infection and increased risk of hospitalization.

Another vaccine against Dengue fever is TVD by Takeda: live-attenuated tetravalent Dengue vaccine (DENV-2 based and recombinant). Dan is currently working on the development of this vaccine as well. The vaccine is in second phase of its development. So far, this vaccine is well tolerated in multiple age groups in Dengue epidemic counties. Prior moving forward, this vaccine will have to go through second phase again and confirm all results achieved in earlier experiments.

Chikungunya disease is caused by a virus that has two transmission cycles and is spread between wild primates and arboreal Aedes mosquitoes (sylvanic cycle); second cycle (urban) involves transmission in human-mosquito-human and has a higher mortality. The development of a vaccine against this disease is taking a lot of time and needs candidates for this research process. The Chikungunya disease originated in Africa and was spreading around the world since 2005. The problem is in protein mutation and lead to higher transmission rates. In U.S., this disease is spread within Gulf states. The NiH VLP vaccine is just starting phase 2.

Zika virus first was isolated from a monkey in 1947 in Zika forest in Uganda. There were numerous cases reported in 2007; epidemic in French Polynesia in 2013-2014. This disease is transmitted by arthropods, and can have perinatal transmission, sexual transmission, and via blood transfusion.

RNA vaccines have several advantages such as rapid response to global epidemics and they are easier to deliver that DNA vaccines. There is a good potential but also several challenges such as vaccine being unstable, and it is difficult to introduce the vaccine to the cells.

It was a knowledgeable lecture. The information provided makes you concerned about safety and health in the world where the virus can be simply transferred by birds. The question I’ve asked was about tips on safety and vaccines required prior visiting Africa as there were a lot of summer programs for students available there. The students were advised to be cautious with water, have long-sleeve shirts available, and mosquito repellent. There is also vaccination available but vaccines requirenments differ depending on the country the student will be going to. But overall, the internship in Africa is a great opportunity for the career growth.

Mapping the uncharted diversity of Arctic marine microbes by Eric Collins

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Eric Collins has been in research projects in different parts of Arctic for several years. He collected samples from a Chukchi Sea shelf and from different parts of Barents Sea (North of Norway), and introduced his audience to the preliminary results. Eric’s bigger term project is to sample all Arctic. Eric also traveled through Greenland (about 400 miles) by skiing. All sampling was done in 2015 expedition.

Eric Collins informed the audience about different kinds of ice and ways that microorganisms interact with ice; talked about the flow of water through Arctic which is the key to understand its properties: the circulation of water takes about 25 to 30 years and it is longer for deeper water layers. There are two main currents that help in water circulation. The modern Arctic has a shallow link to the Pacific Ocean and was 120 m lower 21,000 years ago. Russian rivers provide about 80% of fresh water to Arctic. Throughout the Arctic waters, the temperature, salinity changes, so the conditions for microorganism to survive.

As the climate is changing, the Greenland started to melt and there is not much of ice older than 5 years left in the Arctic. Then, Eric showed a video to demonstrate the change in Arctic size from 1980’s to present. In his project, Eric researched and found a diversity of microorganisms throughout the Arctic waters. Microorganisms differ depending on the sampling place (16S rRNA diversity). Eric explained a “subsurface chlorophyll layer’ which can be found in between nutrients-rich cold water and warm salt water. Then, Eric is planning to map all diversity of microorganisms and he’s already started. This final map will show how microorganisms from one place will differ from another. This map will be like Google Earth; multi-dimensional browsing. More abundance from microorganisms than Archaea or Eukaryotes.

That was an interesting lecture. I’ve learned about oceanography and diverse microbial life in salt frozen waters of Arctic. This research is focused on Arctic territory. After the lecture, I’ve asked Eric if there were any plans for researching Antarctic microbial diversity. I’ve got an answer that the researching Antarctica would be a great opportunity to compare microbial worlds but there is nothing planned in the future for this kind of project.

Microbial Worlds

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  1. Mariah Henderson. “Permafrost: Warming”. I was reading the author’s statement about her work and found out that Mariah participated in this project and learned a lot about global warming and permafrost. The author was impressed on how global the climate changes were and that the thawing permafrost mass became available for metabolism by different microorganisms. The by-products of microbial activity, carbon dioxide and methane, are the major contributors to the “green house” effects and lead to global warming that cause the permafrost to thaw. I found this art work interesting in visual aspect because the author showed the abundant microbial growth on the media. There are lots of bright colors that make this art piece visually attractive for the visitors to stop by and take a look at it.
  2. Nancy Hausle-Johnson. “EMERGENCE: The Warming Climate is Waking Up Sleeping Microbes’. This exhibition is the first one I see that collaborate art and science. It is a great project because most of scientific concerns (i.e. global warming, permafrost thawing) can be expressed through art and brought to public attention. In this art piece, the author researched microbial and fungal diversity on frozen, partially frozen, and completely thawed permafrost. The message to the public is that microbial and fungal abundance and diversity on thawing permafrost can bring potential danger to the environment and the life on the Earth. There can be dormant microorganisms in frozen permafrost that can become active and be potentially harmful as the present population of different species was never exposed to them before. The art piece is aesthetically attractive to viewers being so rich in color, and very organized. The author expressed microbial and fungal abundance as a different in color and shape colonies on various backgrounds. I don’t think that the author should change anything in her work.
  3. Jennifer Moss. “Global transport of microbes: Migration + bacteria grown from dental floss after eating duck for dinner’. “Transmission of information: Hands + bacteria grown from finger swab’. The author used the same concept that we are using in our term project in this class: taking samples from different environment, inoculating the different media, and describing the growth of bacteria. The single difference that the author described the colonies visually through art and painted them. The students will describe microorganisms more in depth: isolating pure culture, identifying the microorganisms through staining and genome sequencing.
  4. If I would be an artist involved in similar project, I would probably use the following microbiological concepts: isolating the microorganism, use different staining techniques, and use fluorescent, laser, or electron microscopy to create bright and vivid art projects.

ExtraCredit: Simon Lax seminar

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Simon Lax presented the lecture “Our Microbial Interaction with Build Environments” where he described his research projects. Simon emphasized the importance of understanding on how microorganisms in the environment can affect us by changing our microbiota and, thus, affect our immunological health. In his research project, multiple environmental samples were collected (with cotton swabs) in order to extract genomic DNA, amplify the gene of interest via PCR, and sequence formed amplicon. 16S rRNA (for bacteria and Archaea) and 18S (for Fungi) amplicon sequencing methods were used to study taxonomy of collected samples. Simon added that his preliminary research has been completed and a Shotgun metagenomic sequencing would be applied as the next step.

In his research, Simon was answering the following questions: Do the microbial communities of home surfaces similar to those on home occupants; how unique the microbial communities are in different homes; what are the major interactions between the home environment and the occupants; how stable the microbial communities on home surfaces. There were samples collected from six home surfaces (counters, floors, doorknobs), three from humans (hands, feet, and noses), also from pets (feet). 18 participants and 7 homes were participating in the experiment (I didn’t catch on how many pets were participating). From the presented results, the person can be tracked in his/her movement in the house via “source-tracking model” because each one of us has “unique microbial fingerprint” (Lax, 2016). For example, “68% of microorganisms on the bathroom door know were originated from the hand #1”, and “much less transfers from noses” (per Simon Lax, 2016). When the occupant leaves the house for several days, microbial fingerprints on home surfaces decline. If to introduce pets to the data, it “mixes everything up because pets are literally everywhere” (Simon Lax).

Simon also spoke about his other research projects: “Forensic insight from Shoe and Cell phone” and “Colonization and Succession of Hospital-Associated Microbiota”. In the results, the person can be matched with the places he/she was walking. As hospitals are dealing with MRSA, different samples from patients’ rooms, floors, and nurse stations were collected for research purposes. The following “hot spots” were found, such as door knobs, handrails, nurses’ pagers and phones, and floors.

In the conclusion, we live in a diverse microbial environment, some of it is a part of us. In the Microbiology class this semester, students will be completing the similar projects: collecting samples from different environments, extracting DNA, and analyze bacterium’s genome sequence with its following identification. Students will present their projects as Simon did (less audience, of course). The lecture was very informative and interesting. The question I had was the following: if the hospitals can benefit with implementation of floor disinfecting barriers? Can disinfecting barriers on the hospital floor reduce the diversity and abundance of microorganisms? It can be very important especially if the patient has a compromised immune system response and unnecessary exposure to microorganisms can harm but not benefit the patient.