Category Archives: Bonus!

Gut microbiota: more awesome than before

Bacteria with telephone, picture via NPR

Who are you gonna call???? (image via NPR)

After 15 straight days of bonus point summaries from students, today brings a special treat as it falls to me to fill the space with content. This was a cool story, spotted via Microbe World from a news story on NPR, detailing work by researchers at Georgia State University and published in the journal Science this week. We are aware in BIO230 of the critical importance of the normal microbiota in helping us to resist pathogens and disease, however much of this benefit is due to the fact that we have developed a state of peaceful co-existence with them (meaning that they do not generally cause disease), and they are able to out-compete the bad guys. On the face of it, this is a rather boring picture, however the research outlined here shows that it is much more interesting and complicated than we might think.

The researchers were interested in developing treatments for a common gastrointestinal infection due to rotavirus. Rotavirus is a highly contagious agent that causes vomiting and severe diarrhea that can last for up to a week. According to the Centers for Disease Control, prior to 2006 rotavirus infections in United States accounted for around a half million doctors’ office visits, with a large number (greater than 50,000) of hospitalizations. Worldwide, there have been about a half million deaths due to rotavirus annually, mainly in children under the age of 5, and indeed young children everywhere are the most susceptible to infection and have the most severe signs and symptoms. Since the deployment of a vaccine in the last decade, hospitalizations due to rotavirus have begun to decrease, and epidemiologists believe that the unvaccinated are now beginning to see some of the benefits of the vaccine through herd immunity.  Currently, there are no antiviral treatments for rotavirus infection, and of course antibiotics actually will prolong the disease course by eliminating the normal bacterial microbiota. The main treatments for rotavirus are to avoid dehydration caused by vomiting and diarrhea. Consequently, there is strong interest in identifying novel, oustide the box approaches for actually treating these types of infection when they occur.

The researchers introduced a bacterial antigen (flagellin), which is the major component of the prokaryotic flagella, under the skin into either healthy mice or mice infected with rotavirus, and observed that healthy mice did not subsequently develop rotavirus when infected (disease was prevented), and in the already infected mice the disease course was stopped (i.e. the mice were cured). The protection was independent of an adaptive immune response, meaning that no prior exposure to the virus was necessary in order to induce the response. The responses to the virus depended on two innate immune pattern recognizing proteins, Toll-like receptor TLR5 and NOD-like receptor NLRC4. The binding of flagellin to immune cells via TLR5 led to the production of a signalling molecule by those immune cells called Interleukin 22 (IL-22), which bound to intestinal epithelial cells and protected them from rotavirus infection. Production of a second Interleukin (IL-18) following stimulation by flagellin through NLRC4 actually eliminated rotavirus-infected cells.

The model being proposed is rather interesting. Bacteria in the gut do not normally cause disease, however components on their surface seem to have powerful immune stimulating capabilities in preventing infection by other, structurally unrelated pathogens. The researchers stress that this study demonstrates the protective nature of flagellin works in mice, which are not humans, and therefore a lot of work still needs to be done to show this holds true for us as well. Fortunately, the basic pattern recognition and signalling pathways are highly conserved between mammals, so there is no a priori reason to expect that these experiments will fail. As indicated in the introductory paragraph, we currently have a pretty good vaccine for rotavirus infection here in the US, which is starting to show real promise in reducing the numbers of rotavirus infection just since its introduction a few years ago. However, the vaccine seems to be poorly effective outside the US, possibly due to genetic variation between strains of the virus in different parts of the world. This approach, if it works in humans, will offer a way to circumvent this problem as it is takes advantage of a generalized innate immune response to a pathogen, as opposed to the specific adaptive immune response promoted by a vaccine. Since it is an innate immune response, there is also no reason to expect that it might not be effective against other virus pathogens that gain access via the gastrointestinal route..

BONUS:  Given the discussion above, list in the comment thread ONE microorganism that might offer this protective effect, along with where you found that information. No repeats. You may have to do some research to find this. Offer runs through the end of Thanksgiving Break!!!!


Happy Birthday to BIO230

Happy Birthday BIO230

At the conclusion of testing, there will be cake

Another year, another 150 or so posts up there on the Internet. I started this project 4 years ago today, with the cryptic posting “Added something to Blackboard,” and found that I liked writing on a regular basis. As the Word Cloud over there on the right might indicate, I am fascinated by the incredible variety of microbial life, and the role that microbes play in health, in disease, and in society at large.  By and large, the vast majority of people who read this are the BIO230 students I see every day, however there is a small but dependable number who visit via links on Twitter and Facebook who have no ties to York College. There are some occasional visitors from various Internet search engines hoping to find help with an assignment no doubt, but this primarily always has been an opportunity for me to help the class extend beyond the classroom.

As all students can likely tell, I can get very excited about Microbiology, and once in a while I go a bit off topic. Things here on the BIO230 blog are a bit more methodical, however I do occasionally enjoy going off on a rant here too. So in that spirit, I hereby declare a “Lightning Bonus” which will be good through 5 PM Friday October 24th. What do you have to do? Go visit these gems from the past, and comment below on this posting about any that might speak to you too. Here are your choices:

An episode of House that pissed me off

An indirect argument I had with a colleague

My attempt to influence the 2011 elections

Evil science, carried out by American scientists

Some just plain bogus science (the recursive offer of 100 bonus points has not been claimed yet)

The state of science funding at present

This one doesn’t count for bonus, but students from last spring didn’t follow directions in this week’s lab


Keeping viruses at bay

Well, it’s heading into flu season, and what’s a Micro prof to do? Get a flu shot, that’s what. As part of the YCP Wellness Fair on Monday during Fall Break, I went over to the Grum and received my flu shot from a very competent nurse, and now am ready to say “Bring it on, Influenza!”

The same day that I did this positive step for public health, I came across a little bit of craziness about the Ebola outbreak, via the science blog Writer Mark Strauss spent some time among the seedier conspiracy theory websites over the weekend, and documented that in addition to the hysteria and mistaken information that is available, there is also some outright disinformation about the Ebola outbreak. Members of the anti-vaccination network have proposed that the spread of Ebola to Texas is part of a concerted government effort to shift attention away from a discredited “whistleblower,” who was going to make a statement about a vaccine/autism link that supposedly had been covered up by the CDC. Another site claims that the initial outbreak of Ebola in discrete regions in Guinea is indicative of a deliberate release of the virus by pharmaceutical companies, so that they could test a secret antidote on an unsuspecting population. Finally, the Vaccine Information Network doesn’t seem to believe that Ebola virus is real, and that the reports in the media are attributed to purposeful misinformation on the part of authorities ultimately “to poison us with drugs and vaccines.”

So after we all take a deep, cleansing breath to clear our minds after that, here’s a bonus opportunity. Simply do as I did up above–go get a flu shot. Document it if you can as I did, by tweeting it or posting it on Instagram with hashtag #ycpmicro, and paste the link in the comment thread below. Offer goes through the end of October, when we should all have gotten our flu shots anyway.

Down with diet

noartificialsweetenersRebecca Donovan (11 AM Micro) is interested in the normal microbiota. I have had a long-standing interest in the role of the gut microbes, and how recent studies have implicated them in a variety of phenomena–see for instance this report about how gut bacteria play a role in mate selection, or this one about a dating service based on gut bacteria. Rebecca’s summary shows that what we feed those bacteria is as important as the types of microbes themselves. Here’s Rebecca’s story, and for those who read to the end, a BONUS opportunity:

A recent article, published on, discovered that artificial sweeteners may be doing more harm than good in your body. Originally marketed to be the ideal solution to those desiring a lower calorie, “sugar less” way to avoid diabetes, recent research has suggested that artificial sweeteners are actually promoting glucose intolerance in the body. If, by this point, I have not convinced you to put down that diet coke in your hand, please read on.

How does this happen?
According to Dr. Eran Elinav and Professor Eran Segal, both of the Weizmann Institute of Science, our gut microbiota, or the bacteria residing in our intestines, are the likely culprits. To confirm this idea, the scientists gave mice water that contained three of the most readily used artificial sweeteners, saccharin, sucralose (splenda), and aspartame (Equal). They found that giving these mice the artificial sugar water promoted development of glucose intolerance to a much greater extent compared to mice only given plain water (Weizmann Institute of Science, 2014). It is also worth noting that mice who were given water containing real sugar developed less of an intolerance to glucose compared to mice given artificial sweetener water. Next, the scientists “cleaned out” the microbiota in the mice through the use of antibiotics. This “clean sweep” of gut bacteria resulted in a return of tolerance to glucose in mice given artificial sweetener water, solidifying the claim of the researchers that gut bacteria are the “prime suspects” in glucose   intolerance brought on by artificial sweeteners.

How do these findings pertain to humans? (After all, we’re not mice!!!)
The scientists involved in this experiment “covered their bases” by gathering a group of human volunteers, who rarely consumed artificially sweetened products, to add them to their diets for a week. After this time, their blood glucose levels would be measured. Their gut microbiota would also be analyzed and measured. The results of this experiment were that most of the participants exhibited an intolerance to glucose after ONLY ONE WEEK of consuming artificial sweeteners. Further analysis of the gut bacteria of participants illustrated  that, with consideration to those whose intolerance levels towards glucose were not adversely affected, that there are two types of gut bacteria living within humans: a type that reacts negatively to glucose resulting in intolerance and a type that has no effect on glucose tolerance (Weizmann Institute of Science, 2014). The researchers involved in the experiment believe that the aforementioned “bad” gut bacteria “turned on” an inflammatory process in the body, negatively affecting the ability of the body to effectively process sugar.

What should this study teach us?
The ultimate question we should ask ourselves is: why would we want to put substances in our body that are proven to be harmful to us? Diabetes and obesity are still, and will continue to be on the rise, in America if we continue to do little to prevent these diseases from occurring. You can take the first step in preventing diabetes and obesity by eliminating  “diet” from your diet. Artificial sweeteners aren’t worth the risks associated with them.

BONUS added by Singleton: in the comment thread, give an example of an association that the normal microbiota has with ANY aspect of human health (good or bad). No repeats, so read what others have put in, and you must give a citation (URL). Don’t worry about formatting of names–I will fix–but do spell them correctly. Offer ends on the end of the day on Friday September  26th.

Brushing your teeth is still controversial

A pretty graph

All time BIO230 blog stats since mid-2011. The two peaks to the right are due to two days only, November 30 and December 1, 2013.

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.


Biofilm (Photo credit: AJC1)

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!

Got my flu shot, did you?

Wearing a band-aid, like a Boss

Wearing a band-aid, like a Boss

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.

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