Category Archives: Bonus!
Thanksgiving Break is generally a quiet time around the BIO230 blog site, as the major visitors are spending time away from the Internet and Microbiology to spend time with their loved ones. Imagine my surprise to open my email over break and see that there were multiple comments to the blog! Student engagement! Discussion! Microbiology talk even when a grade isn’t on the line! However, when I scanned the comments in moderation, I didn’t recognize any of the names, and furthermore they were all for a posting that I had put up almost 3 years ago. What had happened was this: @joedevon who is tech writer and developer based in California came across my posting from 2011 describing the competing commensal relationships between different Streptococcus species in the human mouth.
In the article, I was trying to point out that the web of interactions between microbes is complex, but we could conceivably tweak the interactions in our favor to promote good oral health. @joedevon found my posting via a Google search, and posted the link to the web headline aggregator Hacker News. This lead to an approximately 1000-fold increase in the number of people visiting the blog. The previous best day was in November 2011 on a day that had both a lab report due and a bonus opportunity on the blog, and there were about 120 hits from students that day and I have never come close to that number a second time. November 30, 2013 had almost 12,000 people, several of whom left comments on the blog.
Two commenters remarked about the tenacious nature of biofilms, and the difficulty of removing them. From Craig:
There’s a perfectly good, and reasonablylow-tech, way to break up dental biofilms: using irrigators like Waterpik, or similar gizmos made by Panasonic, Phillips and others. These things are really needle-jet pressure washers that blast apart biofilms that toothbrushes or floss can’t touch, on even the most unexposed dental surfaces.
and from Clay:
Green Tea is the best thing you can do other than floss and brush and maybe use an H2O2 mouthrinse. Green Tea basically disolves the plaque, and does so very effectively indeed.
Biofilms are indeed difficult to remove, and the act of physically brushing does indeed work to break them apart.
Several commenters remarked on the hold that Big Dental has on Western Society, offering insights into the controversy that public health measures bring. From Transfire:
This has been worked out before at the university of florida. It has been possible to all but eliminate cavities for ten years, but $ talks, cures walk.
and these from GogglesNinetynine and Smokes:
There is little evidence that consumption of fluoride increases tooth strength or promotes enamel growth. This is junk science that is forced on citizens because the “nanny” knows best.
…google truth about water flouridation.. it destroyes our teeth…fortunately there are companies now that started making toothpaste without flour in it…
I would point out to Smokes that gluten-free toothpaste is very important for our friends with Celiacs disease. Wait, I don’t think that’s what he meant. I’m sorry guys, but there is a phenomenal body of epidemiological data supporting that small amounts of fluoride promote dental health. The conspiracy argument suggesting that the money involved in prophylactic fluoridation campaigns is somehow lucrative just doesn’t hold water. Look, your average dentist will make far more money from extensive oral reconstruction than he or she does with a twice yearly polishing.
One commenter who passed my moderation test actually spoke to the topic which the original blog post was about; that is, is it feasible to tweak the complex interaction of microorganisms in the mouth to our advantage? Here is a link back to my conversation with Jonathan in the original post. His comment about the diffusion barrier that a biofilm presents is an interesting concept to think about. I think that small molecules might easily pass in and out of a biofilm, however larger molecules might have more of a problem.
This then shows a difficulty with one approach I put forward 3 years ago, where the use of an enzymatic mouthwash to dissociate biofilms that have formed requires that the enzymes have access to the biofilm material. If the biofilm represents a diffusion barrier for large molecules, the enzymes in the mouthwash would need to chew up the biofilm from the outside in, which might not be the most efficient method. Regardless, the tried and true methods of biofilm dissociation likely remain the best options for the foreseeable future.
BONUS: for those that have read down this far, list an organism (at least to the Genus level) that is part of the normal microbiota of the human oral cavity, and include a link to where you got that information. UPDATE! I have finished adding points into Blackboard, so I am calling time, thank you for playing!
The line was about a dozen people deep when I showed up at the Health office on Thursday to get my influenza vaccine. A vaccine against seasonal influenza is recommended by the Centers for Disease Control and Prevention for everyone, except those with certain people including a severe, life-threatening allergy. It is estimated that the risk of an adverse reaction against any influenza vaccine component is less than one reaction per million doses of vaccine , a number which is many orders of magnitude less than the number of people who have a severe complication due to having the flu.
BONUS: In honor of stamping out seasonal flu, I declare a bonus opportunity. Simply comment down below that you got a flu shot and when you got it. If you have a Twitter account, take a selfie of your Influenza Vaccine sheet and post it there with the hashtag #YCPMicro so that I can find it.
BIO230 correspondent Heather G sent me this link from the International Journal of Clinical Medicine, which details a fascinating case study of Gut Fermentation Syndrome. A 61 year old male presented with a long history of intoxication, however there were numerous times when it was clear that he had not been drinking. His blood alcohol levels were frequently noted to be 5 times over the legal limit. The episodes appeared to begin following treatment with antibiotics following surgery, and were more frequent after missing a meal or having a drink the night before. Exam by emergency room physicians in 2009 didn’t know of any way to become drunk without ingesting alcohol, and therefore assumed that he was a “closet” drinker. After referral to a gastroenterology practice in 2010, cultures of H. pylori were isolated from his stomach, and cultures of Saccharomyces cerevisiae and other yeasts were isolated from stool cultures. Following a controlled hospital stay where his blood alcohol levels were carefully monitored over the course of 24 hours following glucose challenge, it was concluded that the alcohol was being produced by his gut microorganisms.
Since this is a topic I could easily be passionate about, I decided to try and learn more. The article linked above had a brief review of the literature, and listed a few primary literature articles describing the phenomenon. My go-to citation finder at the National Library of Medicine was a bust, and turned up little of interest. A search of Google Scholar was perhaps a little bit more encouraging with the number of hits, however again most of the relevant items were not novel. Interestingly, most of the articles that I found dealing with alcohol and fermentation in the intestines dealt with the production of acetaldehyde from ethanol, which is in turn a potent carcinogen. In articles such as this one, the presence of alcohol in the upper digestive tract (presumably from long term alcohol consumption) acts as a substrate that can be further fermented by a variety of microorganisms into the terminal fermentation product acetaldehyde. This compound is strongly correlated with the development of tumors of the small intestine. The production of ethanol as a terminal fermentation product in the mammalian gastrointestinal system appears to be extremely uncommon.
All of the cases in the literature about the topic seem to have several things in common, and patients who develop the condition are typically on a unique diet which contains fermentable sugars, have a diminished bacterial gut flora due to antibiotic use, and have a unique mixture of yeasts which have in turn colonized their system. Fungi do make up an important part of the human gut flora, mainly Candida species, however I can find little evidence that Candida is able to produce ethanol as a terminal fermentation product. Most individuals who exhibit Gut Fermentation Syndrome appear to be colonized with a mixture of yeasts, including Saccharomyces cerevisiae. This is interesting in itself, as S. cerevisiae is a poor colonizer of the human body due to our body temperature, and few articles can be found describing this organism in a disease setting.
And so: an experiment for Science! We will need to start with the yeast. As I prefer a nice IPA, my searching indicates that something like yeast strain 1272 might be a good starter culture. We will need to get the organism adapted for growth in the human body, so we will have to do an enrichment culture at 37 degC, followed by assessment of alcohol production in vitro in the YCP Biology labs. Fortunately, we have in our possession a Vernier alcohol concentration probe, so this is trivial to accomplish. At this point, we will have two options in which to proceed. First, we could jump straight to human trials, however since most BIO230 students are under the age of 21, I think we will go with option two which is to conduct animal studies. We will use outbred CD-1 mice, and administer a broad spectrum oral antibiotic to reduce their normal gut flora, and repopulate with our new IPA yeast via the diet. Control animals will receive heat killed yeast in their diet. We also will administer one of two diets: either a normal rodent chow diet, or a diet which we have supplemented with fermentable sugars–this carbohydrate rich diet looks to be just what we would need. Mice which have been recolonized with our IPA yeast and fed the carb rich diet ought to exhibit behavioral traits that can be measured.
BONUS: For Bonus to be added to your course grade, suggest a method for assessing whether this works in vivo. Do not suggest having the mice recite the alphabet backwards, because unless you are these guys, it isn’t going to work.
We continue our extended series of dangers in the house and the things we eat, with this story from National Public Radio. Long time readers of BIO230 will recall that I am no fan of cleanliness in the kitchen, and quite frankly this report comes as absolutely no surprise to me. Julia Child (pictured here) was a strong advocate of washing out the chicken carcass prior to adding seasoning and popping it in the oven. We are all likely aware that proper cooking of poultry greatly reduces the risk of food-borne disease from the roast chicken. But what about the rest of the kitchen?
It turns out that the act of rinsing out things in the kitchen sink results in the dispersal of huge numbers of microorganisms from the sink. Organisms present on poultry such as Salmonella and Campylobacter can be spread from the sink over a large area, up to at least 3 feet away from the sink. Food safety researcher Jennifer Quinlan of Drexel University is currently promoting a public health campaign to educate consumers of the potential danger of aerosolized pathogens from washed poultry. Her advice? Just make sure that the bird is cooked to an internal temperature sufficient to eliminate food-borne pathogens, and skip the washing step. To illustrate the risks of washing that bird, they show the dispersal of pathogens with “Germ-O-Vision:”
Commenters! For #bonus, identify reports in the media, or in the published literature (for example, via Pubmed) about additional microbiological dangers in the house. I will reward your work with a bonus point in Blackboard, which will also enable you to submit your own blog summaries later in the term for additional bonus! Here are the rules: this only goes through Monday September 9th (1 week to play), you must have something different than what has appeared in the comment thread (no repeats,) and you must include a link to click. Please note, if you have never commented on this blog before, you will not see it appear immediately. I will release it from moderation as soon as I see the comment.
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!
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. Read the rest of this entry