Riddle me this!

I picked up one of the two remaining unknowns from the mystery rack, after all BIO230 students chose their unknowns. I have conducted a series of biochemical tests on unknown #3, but will not reveal its identity quite yet. Here is an opportunity for you to test our your Dichotomous Key, and to earn a bonus point.

Each test was inoculated for 24 hours at 37 °C, and various reagents were added to cultures where appropriate. The appearance of each test at this point is presented below:

IND -> no reaction

MR -> red color

VP -> yellow color

CIT -> green color

PHE -> green color

LYS -> brown color

GEL -> liquid

SUL -> black color

URE -> pink color

You may infer results to Carbohydrate Fermentation tests by the following:

MacConkey’s Agar -> white colonies

Triple Sugar Iron Agar -> red slant, yellow butt, no cracking of agar

Here is the Bonus opportunity; using your dichotomous key and the above results, determine what Unknown number 3 is. To preserve the fun, email me your answer! Note that this special Bonus opportunity is only available until the end of Spring Break on Monday evening April 1st at 6PM.
UPDATE! Unknown #3 was Proteus mirabilis. The combination of the urea and indole tests would have been a good tipoff. Thanks to all who played!

Sexual transmission of cowpox

Site of injection of vaccinia, the vaccine for smallpox, several days after the injection. (Photo credit: Wikipedia)

Well, the title stretches this case study a bit, but it is all about drawing the reader in. I came across this story via the ever enlightening Morbidity Mortality Weekly Report, published by the Center for Disease Control and Prevention. The latest issue describes a local outbreak of vaccinia (cowpox) infections during June 2012. The first patient was admitted to a private hospital, reporting painful skin lesions. Superficially, the lesions resembled those of cowpox, and the patient reported sexual contact with someone who had been vaccinated with this virus, suggesting a route of transmission. The San Diego Public Health Laboratory then detected non-smallpox Orthopoxvirus by polymerase chain reaction (PCR) analysis to confirm the diagnosis. The patient was then treated with vaccinia immune globulin intravenous (VIGIV), a form of serum therapy, or passive immune protection against the infection. The lesions resolved without complications.

A second patient also reported skin lesions a few days later, and follow up of the case indicated that this individual’s only link to the case was sexual contact with the previous patient. This was a tertiary transmission event, from the initial vaccinated individual, to the first patient, then to the second patient. Again, vaccinia infection was verified by the Public Health lab, and treatment with VIGIV resulted in full resolution. Patient Zero was a civilian who had received the smallpox vaccine as part of the Department of Defense vaccination program. Epidemiological investigation indicated that he had only been in contact with the first patient. All patients were monitored to ensure no further transmission had occurred, particularly to at risk individuals, such as those with immunocompromised status, pregnant women, or people with chronic eczema.

Turning seawater into gold

English: Crystalline Gold (Photo credit: Wikipedia)

Via a number of news sources, and published in Nature Chemical Biology: a report describing new research with a metallophore bacterium. Researchers at McMaster University in Ontario, Canada have been looking at microorganisms that have been associated with biofilms growing on gold nuggets. Gold, like many heavy metals, is toxic to many organisms. Consequently, it was surmised that any microorganisms that are able live in close proximity to these materials must have a mechanism for being able to survive by them. Sequencing of organisms in gold biofilms identified two species, Cupriavidus metallidurans and Delftia acidovorans that made up over 90% of the biofilm associated microbes. The researchers decided to focus on these two species in order to identify any potential mechanisms that they might have had to assure survival in the presence of lethal levels of soluble gold. 

RoboPOOP

It’s been 2 years since I’ve used this graphic, but it feels appropriate

Via National Public Radio, and as published in the medical journal Microbiome, here is a study for you to read over lunch. Fecal supplementation therapy has been utilized occasionally for more than a decade. A posting from 2 years ago showed the efficacy of fecal transplants in patients suffering from chronic Clostridium difficile infections, and a student guest posting from last semester offered an improvement in the technology with a preliminary analysis in mice.

The principle is rather easy to understand; C. difficile generally causes disease in situations when it is a major component of the bacteria, after having outgrown the normal bacteria at that site. If the balance between the numbers of disease-causing bacteria and normal bacteria can be shifted back, disease should go away. Fecal transplants and fecal bacteria supplementation therapy are designed to do exactly this, and this is also the principle behind probiotic food supplements with regards to their potential contribution to digestive health. The problem with most probiotic bacteria (the kinds you get in yogurt or in pill form as a dietary supplement) is that they do not survive the passage through the low pH environment of the stomach. Consequently, fecal transplants and fecal supplementation therapies need to bypass the stomach to be useful, and in general bypass the “ick” factor with patients. 

The researchers from three universities in Ontario, Canada performed a molecular analysis on the fecal bacterial profiles of several healthy volunteers. Non-pathogenic organisms were isolated in pure culture and grown in the laboratory in bacteriological media. Pure cultures of organisms were then mixed in defined amounts, based on the molecular profile analysis of the healthy volunteers, to produce a mixture of microorganisms in approximately the same proportions that they would be found in the lower digestive tract. This mixture was introduced into two patients suffering from multiple drug resistant C. difficile infection (CDI) during a routine colonoscopy procedure.

Typical patient course; RePOOPulate procedure was done at the second green arrow

The figure summarizes one of the patient histories, treatment regimens, and medical outcomes. The trial procedure was done with two patients with similar disease histories, and in both cases the patients were completely symptom free at 32 weeks post-procedure. The researchers are following up this pilot study by enrolling additional patients, and by also examining the long-term persistence of the RePOOPulate bacteria in animal models with administered antibiotics. The authors note that treatment options in patients with multiple drug resistant C. difficile infections are essentially non-existent, and that repopulation by normal microorganisms represent the most effective approaches today.

A quick bonus for one lucky recipient who read down this far; why do you think I picked the graphic up at the top? Comment below!

Welcome to Microbiology!

Portrait of Antoni van Leeuwenhoek (1632—1723). (Photo credit: Wikipedia)

This is the class blog for BIO230, Microbiology. I will typically update this site several times a week, with articles and news alerts that I find from a variety of sources. Sometimes postings will be very topical to health-related issues here at home, while sometimes they may only appeal to those of us below the age of 5. Sometimes I get so angry that I use inappropriate language, other times I may just update with a cat. If you don’t want to miss a posting, make sure that you subscribe by clicking the “Subscribe me!” link over there on the right. You won’t regret it, and you may even be the first to know about sooper sekrit bonus opportunities.

Here’s the first: to add a bonus point into the new Blackboard column labeled “Bonus points,” comment in this thread with 1) the topic in BIO230 you are most looking forward to, and 2) the topic in BIO230 you are most apprehensive about. Note that it would be useful to actually look at the syllabus to do this, and to perhaps thumb through the table of contents in Bauman 3rd edition. I will not count any answer that says “all of them.” You’ve got to make this worth my time, folks.

STD parasites infected with viruses

Several parasites of humans

Last month’s case study about virophages, where a species of amoeba was found to be infected with a virus, which in turn was infected with a virus, was interesting but really pretty much an exercise in “Wow! That’s interesting” as opposed to something that might feel clinically important. Not so today! Via Boing Boing, from an article on Live Science, a report about viruses that infect Trichomonas, the causative agent of a very common venereal disease.

Trichomonads are interesting in their own right; they are eukaryotes like us, classified in the broad group of single-celled flagellated protozoans, however they are anaerobes. A little cursory research indicates that this class of protozoans lack fully functioning mitochondria. This suits the lifestyle of Trichomonas vaginalis, which colonizes the surfaces of the vaginal tract in humans. It is then transmitted between sexual partners and can spread through the population via non-monogamous means. On its own, Trichomonas infection is not particularly severe, however women infected with this organism are more susceptible to other STD infections, and pregnancies are significantly more risky with a high frequency of preterm complications and miscarriages.