Journal of Microbiology: Taxonomic and physiochemical analysis of Kocuria rhizophila

Dan Mulkey

I isolated a strain of Kocuria rhizophila  from a patch of atopic dermatitis on my leg, in an effort to better understand the microbiotic component of the condition. There was not much existing information on this strain, so it was interesting to piece together what exactly Kocuria does different.

Image Credit:


Link to paper:

A2: Rockland County orders public space ban for those diagnosed with measles

NPR, 4/17/2019



In response to the New York City measles outbreak, Rockland County, NY has issued an order banning those diagnosed or exposed to measles from all places of public assembly. Over 550 confirmed national cases, including 186 in Rockland and 329 in NYC, have been reported this year. This marks the second largest outbreak since 2000, the first being in 2014 (667 cases) [1]. CDC officials report that the outbreaks have been associated with Orthodox Jewish communities and other travelers returning from Israel. The vaccination rate for children in Rockland is only 72%, much lower than the 90% recommended for herd immunity to be effective.


We have covered the importance of herd immunity in class, and the dangers of an unvaccinated populace exposed to a pathogen like the measles virus.

Critical Analysis:

Though many of the Health-tagged stories on NPR have an obvious political slant, this one’s information is surprisingly clear-cut. It explains the rising toll of the infection, the cause, and the societal consequences, maintaining all this within the context of the infection.


How can the public be better informed about the benefits of vaccination and the need to take protective measures against pathogens, without victim blaming, ad hominem intelligence insults, or appealing to the cult of scientism (which would further alienate those hesitant to get vaccinated)?

Additional Info:


Art Project: Rise of Vilithrax

Dan Mulkey

To preface, I have been the Dungeon Master for my friends’ Dungeons & Dragons campaign this semester, which involves creating worlds and adventures, then playing them out with characters and dice within the rules of the system. While reviewing viral structure in class, I was struck by the polyhedral nature of the viral capsid, noticing that it was evocative of a D20, the most prolific die in the game and the most evocative of D&D as a concept. Using a bit of copper wire and a D20, I fashioned this small bacteriophage figure with literally $2 and 10 minutes of my time.

Of course, even I would consider this barely worth a C, so I also decided to take a bit of viral inspiration and fashion a Dungeons & Dragons encounter designed after a viral outbreak.


The problem I ran into was it being difficult to design a monster for D&D that you can’t hit with a sword, so I created a few variants on the bacteriophage design:

The first I dubbed a “crawler”, a bacteriophage without a tail, roughly the size of a small dog. These would hunt down nearby creatures (symbolizing cells) and attack with a small mouth on their underside. They would then inject “viral DNA” which, after a “lag phase”, would assemble itself into a new crawler using the host’s biomass, slowly making them sicker and more invalid. It would then burst out of the host’s chest in a spray of viscera, killing them instantly. This represented a lytic viral attack. Another variant, the “acolyte”, would have the viral DNA incorporated into their own biomass, evolving them into a sort of bacteriophage/humanoid hybrid, with their tail hidden under robes and manifesting tail fibers like a viral centaur. This was intended to be representative of a lysogenic cycle, though in this case the host is empowered by the incorporation of viral DNA.

Over the course of a 6 hour session, the heroes successfully quarantined the city, isolated healthy survivors, and detained Vilithrax, the mad priest who initiated ground zero of the infection in a crowded church. Time will tell if some phages escape the city and wreak mayhem in the rest of the world.

A2: Rubella cases exceed 100 in single week

NHK World, 3/5/2019


Japanese health officials have reported 109 cases of rubella in the week of February 18-24th. This brings the total 2019 rubella cases in the country to 650, four times higher than the same period last year. Officials predict that this year may be comparable to 2013’s record year of over 14,000 cases. The national government has begun offering free vaccinations to males between 39 and 56, an age group that did not receive childhood rubella vaccinations. In addition, some municipalities are offering free vaccines to women who may become pregnant and their families, in order to curb potential (visual, auditory, and cardiovascular) birth defects.


We have just begun learning about viral structure and function in class, and how (for lack of a better term) virulent they can be. Rubella is another example of an airborne pathogen, and it was thankfully eradicated from the US in 2004, according to the CDC.

Critical Analysis:

This, as with other similar stories from NHK World, are meant as informative public broadcasts rather than in-depth scientific literature. It focuses mainly on raising public awareness of, and government response to, the outbreak. It does, however, touch on the complications rubella can present for pregnant women.


How prevalent are airborne viruses, and why is everyone not infected all the time by an airborne pathogen without the biological constraint to maintain life?

Additional Info:

A6: Painting with Microbes

Dan Mulkey



For the last year and a half or so, I’ve visualized my “capacity to love” as the tender of an oasis in an impassionate desert. The oasis must be kept bountiful, of pure intent, and shared freely with the thirsty. The  S. marcescens unfortunately did not turn the dunes as red as I would have hoped, and I realize now I should have used some more contrast, as the water features are barely visible against the rest of the structures. It’s a shame we had no blue/green cyanobacteria. I also should have gotten a refill on the  C. violaceum, as the palms got a little sparse.

I used TSA for this one because it is a non-differential medium and the differential agars would have produced an effect that would have muddled the overall picture (though in retrospect, the MacConkey agar may have produced more contrast)

Sun Ascendant

I wanted to do a sort of “2001: A Space Odyssey” thing here, with the sun rising over a silhouetted black horizon and casting a hazy glow.

To this end, I used  S. marcescens for the sun  (which was not technically a fermenter, but had a bizarre reaction with the differential MacConkey agar which triggered the pH pigment change). Unfortunately, I overdid it on the sun streaks and the entire agar changed color instead of just the area around the center.

A2: Pigs culled in Shiga after swine fever outbreak

NHK World, 2/07/2019

Summary:  Roughly 700 pigs have been culled at a farm in Omihachiman, Shiga Prefecture (滋賀, middle left on map) after an outbreak of  Pestivirus CSFV, a Group IV virus responsible for classical swine fever. While this pathogen is highly contagious among domestic and wild swine and known to cause symptoms including fever, skin hemorrhaging, convulsions, and death [1], humans are not susceptible. The carriers were among a total of 60 pigs shipped from Aichi Prefecture (愛知, center bottom) to four other prefectures on January 31st. The first case of CSF in Japan in 27 years was discovered September 2018 in Gifu Prefecture (岐阜, center top), spreading from there.


While we have not yet covered viruses or communicability in class, the precautions we take in lab to avoid communication of our unidentified strains is likely an afterthought on commercial farms. It’s no wonder that crafty and deadly pathogens could have such a devastating effect on food supply chains.

Critical Analysis:

This article is written more as an informative story than a piece of scientific literature. However, it does provide reliable information on what  Pestivirus CSFV is and the effects it can have. While it has been reportedly eliminated in many western countries, including America, Canada, and Australia, cases still arise such as East Anglia, United Kingdom in 2000 [1].


What makes pathogens selective in their attacking, and is it truly more advantageous to specialize and “hide under the radar” rather than diversify to obtain the maximum potential number of hosts?

Additional Info:


Kiyoshi Shiga

Shigella dysenteriae, as well as the other bacilli in the genus  Shigella, are named for the Japanese physician and bacteriologist Kiyoshi Shiga, who first isolated  S. dysenteriae around the turn of the 19th century. These bacteria are the most common causes of dysentery, specifically coined shigellosis in cases caused by Shigella bacteria. Shigellosis causes diarrhea, fever, abdominal pain, and rectal tenesmus, and has the potential for life-threatening complications such as intestinal perforation, sepsis, and hemolytic uremia. As the WHO reports 80 million cases and 700,000 deaths per year, 99% of which occur in developing countries, Shiga’s discoveries and work have been instrumental in preventing the proliferation of this horrible disease in the first world.

Kiyoshi Shiga was born in 1871, in Sendai, Miyagi Prefecture, Japan. Entering the Tokyo Imperial University School of Medicine in 1892, he was mentored by Dr. Shibasaburo Kitasato, famed for his discovery of tetanus antitoxin and work on  Yersinia pestis in Hong Kong. As a member of Dr. Kitasato’s Institute for Infectious Diseases, Shiga worked tirelessly on the search for the cause to Japan’s 1897 dysentery outbreak (90,000 cases, 30% mortality), finally isolating a gram-negative bacillus that agglutinated on dysentery patient serum. He developed and distributed intravenous and oral vaccines for the pathogen, using himself as a test subject. He spent four years in Paul Ehrlich’s lab at the  Institut für Experimental Therapie in Frankfurt, Germany, where he worked on early chemotherapy methods. To global acclaim, he presented his work on shigellosis in Manila in 1906. Due to restructuring of the Institute for Infectious Diseases, he left with Kitasato to form the Kitasato Institute in 1914. He served as a medical professor at Keio University in Tokyo, as well as the director of National Hospital of Seoul, Korea, and the President of Keijo University in Seoul. In 1931 he returned to Japan to continue his research into dysentery and tuberculosis at the Kitasato Institute until 1945. He died in 1957, at 85 years of age.


World Health Organization. 2005. Guidelines for the control of shigellosis, including epidemics caused by  Shigella dystenteriae  Type 1. ISBN 9 24 159330X;

“Shigellosis.” Wikipedia, the Free Encyclopedia.  23 Aug 2018.

Trofa A., Ueno-Olsen H., Oiwa R., and Yoshikawa M. 1999. Dr. Kiyoshi Shiga: Discoverer of the Dysentery Bacillus. Clinical Infectious Diseases 29:5; doi:10.1086/313437

A1: Intro, Dan Mulkey

Hello all,

I’m Dan Mulkey, 5th year Bio/Japanese major. I’m hugely interested in health and how to maximize the potential of the human body, so I’m hoping we cover some nutritional applications of microbiotic science. Very much a “big picture” sort of guy, but we wouldn’t have big pictures without all the little stuff that makes it up.

Here’s to a good semester!

Me in Enoshima