The Germ Guy: Confessions of a Mercurial Microbiologist



A Virus With An Avengers Twist…

Over the last few years, there have been quite a few movies based on comic books and several have been standouts. One of the most successful franchises is known as…


This team has saved the planet countless times both on page and silver screen. History has shown they work best when together, but the members do have a habit of splitting up on their own. When they do, the outcomes are not as spectacular nor as Earth-changing, but they do leave a wider impression on the people and sometimes, can help make a spin-off superhero movie a success.

I digress…

The concept of splitting up is not all that uncommon on an evolutionary basis. Higher order animals do this regularly especially in horror movies and…

Split-UpScooby-Doo Episodes

Not to mention, bacteria have been doing this for as long as they have been around.

biofilmSplitting Up For Form Biofilms

But this trait never has been seen in animal viruses. This should make sense as these biological entities are designed to act as individuals, not as a team. The components need to stay together in order to survive.

Yet, thanks to a recent discovery, that viral view may change…

A Virus That Splits Up

What you are looking at are images of a single virus species, known as Guaico Culex virus, or GCXV. It was recently discovered in mosquitoes (Culex) in Trinidad (Guaico). The different colours, much like the markings of the Avengers, happen to be different segments of the virus’s genetic code. As you can see, they are scattered all over the place.

When you group the photos together, you end up with something like this…

gcxv-infectiousAn Examination of All Segments

Look for any cells appearing brown. These have all the segments of the virus and are unfortunately doomed. The green, orange, and blue cells, are going to survive even though they contain some of the segments. That is, until the brown ones burst and spread segments all over the place.

While the finding is remarkable from an evolutionary perspective, the reason behind this phenomenon may not be as easy to deduce. Even the researchers who discovered the trait weren’t quite sure why this virus seems to split up.

There is, however, one theory and it has to do with something the Avengers enjoy exploiting…

hulk-lokkiHULK SMASH!!!

Numerous segments of the virus, much like members of the Avengers, head out in search of enemies to defeat. When they have found the targets, they engage. However, the superhero may not have enough power, energy, somersaults, arrows, whatever, to win. Same goes for the virus. It just doesn’t have all the machinery to kill. But then along comes the Hulk to save the day, usually with a good smash. In the same way, the other viral segments show up and eventually, the virus survives.

While this premise is still a theory, there is at least one factor the virus doesn’t need to worry about when it comes to assembling…

hulk-thorOnly The Hulk Smashes Indiscriminately

If you want to read more on the GCXV discovery and the fascinating mechanism of splitting up, you can find the entire article here: A Multicomponent Animal Virus Isolated from Mosquitoes



#AskTheGermGuy – What Exactly Is Bagpipe Lung?

The bagpipe…


piperA truly majestic instrument

The sound is unmistakable and, having known a few pipers myself, those who play are unique and usually unforgettable.

I received a note from one of these wonderful musicians earlier this week asking about the nature of a recent story making the headlines. A British bagpiper came to a rather unfortunate end as a result of lung disease. He apparently had died of a rare condition called “Bagpipe Lung.”

I went in search of the original paper and found it in the journal, Thorax:
Bagpipe lung; a new type of interstitial lung disease? — King et al. — Thorax

The story of the individual’s plight was quite sad to read. Doctors tried to find any reason for the illness but came up empty. He wasn’t a smoker nor did he have any outward signs of infection. They tried a number of antibiotics and antifungals yet nothing seemed to help.

After he died, the cause was eventually determined. He had suffered from a condition known as hypersensitivity pneumonitis. In essence, his lungs had shut off in the same manner as an allergic response.

Knowing that the person was a piper, the doctors wondered if the instrument could have played a role in the condition. They took samples from various areas of the bagpipe, including the bag, the neck, and the reed protector. They cultured them and waited to see if their theory was correct.

Here’s what they found…

This is not pretty…

All the samples showed the presence of fungi, some of which were potential pathogens. For the authors, this made perfect sense. As they state in the article…

“The moist environment of bagpipes promotes yeast and mould contamination, thereby making the chronic inhalation of offending antigens a likely trigger.”

For any piper, these words are disturbing to say the least. The bagpipe is a delicate instrument and removing microbial life may be difficult. Making this situation worse is the lack of any guidelines on how to properly clean the various parts.

When I shared this information with the piper, I was pleasantly surprised to hear he was not at all worried – it turns out he was once an ER nurse. Instead, he shared with me his regimen for cleaning:

“Good old soap and water and replacing the hemp that seals the joints on the stocks reasonably regularly.”

Of course, if you want a more scientific option, there is a study from 1958 that says pretty much the same thing. You can read that here:
Bacteriological and Cleaning Studies on the Mouthpieces of Musical Instruments

Another excellent option is to keep regular visitations with a doctor to keep track of lung performance. Hypersensitivity pneumonitis develops over time and can be reversed if caught early. A doctor can also make referrals if necessary such that any warning signs can be diagnosed and treated.

Whether you choose to pipe regal refrains or something that might well…

Rock You…

I hope this information will help raise awareness so everyone who chooses to pick up the bagpipe can keep those resplendent reeds a-roaring!


Biome, Genome, Microbiome…Houdinisome?

As I wrote in The Germ Files, science loves suffixes.  The most recent fad has been the addition of the letters ‘ome’ to a root word to denote the totality of all involved molecules. Biological entities become biome, genetic material gives way to genome, and microbes beget the microbiome.

But in a paper last week, another -ome surfaced…

houdini2The Houdinisome!

Going by the rules of the -ome world, one might think this refers to the totality of escape artists around the world. But this isn’t the case.

Instead, the word refers to a group of viral components known as ‘ejection proteins.’ You might be wondering how the two have any connection, let alone justify the creation of another -ome. Here’s what the authors have to say:

“The exit of these internal proteins from the capsid represents a remarkable case of molecular escape artistry that presumably depends on, among other factors, the locations of the ejection proteins at the time DNA release initiates. (Harry Houdini, the doyen of escape artists, had a vaudeville act in which he would extricate himself from seemingly impossible states of confinement—hence, for elusive proteins, the term “Houdinisome.”)”

If you want more information, you can read the paper here:
Localization of the Houdinisome (Ejection Proteins) inside the Bacteriophage P22 Virion by Bubblegram Imaging

I can see where the researchers are going as it does make sense in a microbiological sense. I just wonder if this invention might signal the apex of the -ome fad.

In other words, with the advent of the Houdinisome, have scientists finally…

jumpshark2Jumped The Shark?
(if you don’t know what this means, Google it)

This moment might be the impetus for the scientific community to examine a new suffix. Or, more likely, the action may lead to even stranger names with even less impact on the subject actually being studied. After all, even Henry Winkler – the actor in the video above – somehow managed to jump the shark twice.

jumpsharkStill one of the best scenes on TV

What do you think is the future of the -ome?

Are You Ready For A Health Tea-volution?

Most people upon hearing the word, tea, think of this…

teaA nice cuppa!

But the giant tea company Tetley, wants you to think of tea in a different light. They recently began an exploration of tea technology and uses over the coming decade. They’ve aptly named it…

future-tea1(hashtag included)

You can read the entire concept here:

Some of the ideas seem based in the current coffee culture and the rise of do-it-yourself wellness. But some are an apparent throwback to traditional medicine with a modern twist.

For centuries, medicinal teas have been used to help manage and/or cure diseases of all kinds. They may not have been as effective as today’s medicines but research has shown many blends did have chemical constituents capable of alleviating certain types of ailments. An entire branch of scientific research continue to learn how the remedies of the past have value today.

But Tetley wants to take it one step further. Instead of going the traditional route in which a healer determines the best concoction for the right symptoms, the company proposes, well, this…

tea-future-2A personal remedy tea-making machine.

The concept involves reading personal data, such as vital signs, to determine if there are any problems with overall health. Then, using a computerized algorithm, the right mixture of chemicals can make the right brew for you. Add in some medicinal ingredients and the concoction can deliver remedies without the need for a pill.

Of course, this may all seem like science fiction and the company admits this is a look forward to 2026. However, some of the technology is already in place. One such example is this…

A wearable vital signs sensor

This small but powerful band was designed to help monitor people during the Ebola outbreak in Africa. The device can track a number of parameters including:

  • Heart rate
  • Pulse synchronized oxygen saturation
  • Temperature
  • Respiratory rate
  • Depth of respiration
  • Motion/position

The information can be sent to a computer via USB however a Bluetooth version is in the works. You can read more about the technology here:

Just imagine if the computer receiving the information was contained within the tea-making machine. The result would be akin to a personalized traditional healer (in digital format) able to provide the right combination of herbs, medicines, and fluids.

Now of course, there is one obvious question not addressed in the document…


Would you trust a computer with your health?

Finding the answer to this question, I’m afraid, may be no cup of tea.

Cucumber Mosaic Virus: Pathogenic Philanthropy or Devious Domination?

Most people think of viruses as nothing more than parasitic organisms looking to kill its host. This limited view doesn’t take into consideration the sustained survival of the pathogen. After all, if the host dies, so will the virus. That’s why these organisms need a large supply of unwitting – and usually unwilling – victims.

Human viruses have it pretty good thanks to all that shedding we do over the course of a day. But the same cannot be said for plant viruses. Plants don’t move and for the most part, don’t share their vital fluids without some help. Without outside assistance from creeping plants or insects, the future can be quite dire.

Which brings me to this interesting pathogen…

cmvIt’s called Cucumber Mosaic Virus (CMV)

You may not have heard about it but you may have seen it in action…

cuke_mosaicThis is what it does to cucumbers

But these plants are not the only host for this virus. The pathogen can infect over one thousand different species of plants including one we all cherish…


The most important route of spread happens to be aphids. These little insects can pick up the virus and spread it to another healthy plant. But there’s a problem. When an aphid sees an infected plant, they tend to say…

nopeCan you blame them?

So the virus has developed an ingenious method to get the aphids to come. They lure the insects by changing the way the plant smells. It’s a rather complicated process so I won’t go into the details. If you are curious, you can read more about it here:

This game-game changing trait makes CMV even more troublesome than once believed. Yet, there are even more surprises in store. In a study released today, it seems the virus can attract more than just aphids. They also seem to lure in…

bee-tomato Bees…

At first glance, this may seem reasonable as bees are pollinators. They would help to spread the virus. Except bees don’t actually come into contact with the pathogen. Attracting them seems to have no value to virus survival. Which brings up the question…

Start_With_WhyWhy would the virus do this?

There are two trains of thought as to why this phenomenon occurs.

The first is a form of pathogenic philanthropy. When the bees come near a tomato plant, their buzzing wings tend to improve self-pollination. The number of seeds per fruit – yes, tomato is a fruit – increases and the plant population may increase.  The buzzing may also help cross-pollination giving the population an even greater chance for sustained success over the generations.

When you hear this side of the story, you might think…

cat-niceWho doesn’t love a virus that gives back?

As for that second theory, it’s as you might expect, devious domination. The virus needs a sustainable crop of hosts to maintain survival. Bees are the perfect vectors as their activity has no link to the virus itself. As the number of tomato plants increase, the virus has a better chance at survival.

But there’s even more malice to this method. Some tomato plants can resist the virus making survival less likely. By attracting bees to the infected plants, the virus is effectively ensuring resistance is diluted out of the tomato population. This would allow the virus to completely dominate the environment in a dastardly and definitively despicable way. You could say…

pres-snowPresident Snow Approves
(if you don’t know who this is…ask your kids)

While both theories are possible, neither has been proven as interviewing a virus tends to gain few answers (they are always mysterious that way). However, if one is to bet on the reason behind this strange action of the virus, I suggest the latter is correct. Considering self-sustainability drives pretty much all biological life, selfish preservation always, um, trumps, benefiting others.

May the odds be ever in your favour…

PS – if you want to read the article to get a better sense of the work done, you can find it here:

Clinical Trials 2.0 – Finding Volunteers Using Facebook

You’ve probably heard of clinical trials. They are frequently mentioned in the media whenever there is a new advancement in medicine. But you might not know they are randomized, meaning the participants are not specifically chosen. Depending on the goals of the trial, certain populations are targeted but researchers do not know in advance who might be involved. It helps to keep the results fair and objective.

Of course, to get a large enough size of possible volunteers, those in charge of conducting trials need to recruit members of the public. They do this using advertising, usually in newspapers and other traditional media. For the most part, these recruitment documents are rather boring but at times, they can be inventive…

clinical-trial(Who wouldn’t want to contact this researcher?)

But now there may be another way to recruit participants using social media. Last month, a team of Australian researchers reported on how they were able to acquire volunteers using something we have all seen…

The Facebook Ad

At first glance, you might not know what exactly is being offered other than a ten dollar gift voucher. That’s the plan…they want you to wonder. When you click on the link, however, you won’t be taken to some clothing manufacturer or travel booking agency as you might expect. Instead, you end up here…

vaccine-studyThat’s right…a vaccine clinical trial.

The paper examined the effect of this type of advertising over the course of four years, from 2011 to 2015. In addition to the advertisement above, they also had other slightly more informative ads like this one…

You might have even seen the advert and clicked on it.

Over the course of the four years, the ad had 55,381,637 impressions with a reach of 984,159 people. As for how many women actually clicked on the link? It was rather small at 23,714, or about two and a half percent.

The click rate was pretty low in comparison to standard advertising, which has about a three to six percent return rate. Yet, for the authors of the study, this was significantly higher than other methods as they ended up with 919 potential volunteers. Almost four-fifths had seen the ad and made the choice to apply. The others were either referred by friends or read the advert on a friend’s wall.

As for the cost, it was just over 22,000 Australian dollars, or about $24 per participant. For the authors, this was rather inexpensive burden for this type return. They had what they needed and more importantly, developed a method which others can use to improve their own clinical trial recruitment.

In light of this study, this seems like a win-win situation. But I have to ask…would you click on a Facebook post advertising a clinical trial? Maybe it’s just me but that still seems a little sketchy.

Let me know your thoughts…

Oh, and if you want to read more on this concept, here’s the link to the paper…
Targeted Facebook Advertising is a Novel and Effective Method of Recruiting Participants into a Human Papillomavirus Vaccine Effectiveness Study

Measles And Music Festivals Make A Malicious Mix

Thanks to the fearful prophesies of an infectious Olympics, the world is awaiting any signs of the warned outbreaks ranging from Zika to norovirus. The premise does have some value as any mass gathering, such as the Games, increases the chance for infection spread. Yet, so far, it’s been relatively quiet.

The same cannot be said for another kind of mass gathering…

glastonburyThe Music Festival

In the United Kingdom, there has been a rise in infections coming from festivals including one of the largest, Glastonbury, pictured above.

While this might not be a surprise, the type of infection may raise a few eyebrows.


In the last few months, a total of 36 cases have been reported all sourced to a musical gathering. While this may be enough to make your head itch, the situation gets worse as some people didn’t catch the virus at the festival. Instead, they were already infected and yet still decided to go to the event to spread the joy and the virus.

The reaction to this revelation has been mixed but can generally be summed up with:

Who could be that unaware of the consequences?

But the worst is yet to come….

Most people believe measles only infects children. But the virus can attack anyone who might happen to be vulnerable. In these cases, the average age of those suffering is 20. The oldest person was…

42(If you don’t know who this is…ask your local fanboy or fangirl)

This information is rather startling. The slowdown in measles vaccination has been ongoing for only about 15 years. The older patients most likely would have received their first shots but perhaps not the boosters necessary to maintain protection throughout life. This suggests an even greater population may be vulnerable without even knowing it.

The solution may seem easy enough: get a booster no matter how old you are. But, that’s not all that easy in this day and age. With vaccine hesitancy continuing to rise, the idea of a mass vaccination campaign might end up being fruitless and be met with resistance. But that’s not all. People simply may believe they are safe from prior shots. They would feel like they don’t need to get the boosters.

All of this leaves Public Health England in a bit of a bind. To see how they have decided to move forward, you can check out their recommendations here:

If you think you have a better idea, why not share it here. I might even offer my own rather unconventional proposal…


Can bacteria really live in dry flour?

Earlier this week, I had an excellent Email question regarding a foodborne outbreak in the United States. You can read more about it here: Multistate Outbreak of Shiga toxin-producing Escherichia coli O121 Infections Linked to Flour

That’s Right…Flour

The question was simple enough. How can bacteria live in this environment? After all, one of the three needs for growth – water – is missing.

The premise makes perfect sense yet, once again, bacteria seem to know how to break the rules. Many species can indeed survive drier areas. When it comes to flour, E. coli can survive for over 6 months. If you don’t believe me, check out this report:

One section dealing with bacterial growth in various foods states:

Yersinia pseudotuberculosis, Salmonella enteritidis, and Escherichia coli O157:H7 can survive in flour and infant formula beyond 180 days. Survival in flour was best under refrigerated conditions.

The explanation behind this apparent paradox lies in the nature of the flour itself. While you might not see water, it is still there.


In almost all areas of the world, water exists in the air in the form of humidity. Materials, like foods, may also have water content in the form of vapour pressure. This can be measured and compared to the vapour pressure of distilled water. The result is known as water activity (aw).

Water activity ranges from 0.0 (bone dry) to 1.0 (distilled water). In food safety, water activity is incredibly important as it can determine whether a product is at risk for microbial growth. For fungi, the activity needs to be above 0.7. For yeast, it’s 0.88. For mold, 0.80. As for bacteria, that number is 0.91.

Many food have been tested for their aw and lists now exist. One such example can be found at the FDA:

So, how does this relate to the flour outbreak? If the water activity was above that 0.91 threshold, then the bacteria would not only survive but also grow. If there were no antimicrobial steps in the processing stages, those bacteria would find their way into the food production chain and eventually to your counter.

As to whether water activity played a role in this particular outbreak, only further investigations will tell. There may have been other contamination events during the flour’s food continuum. But when it comes to the question at hand, as long as you have that water activity over 0.91, you can potentially have bacterial growth.

The Curious Case of Cola To Combat Swimmer’s Stomach

A friend sent me a text message asking a very strange question:

“Can cola kill pathogens after swimming?”

It seemed like an easy answer:

Swimmer’s stomach is a rather annoying condition whereby bacteria swallowed from natural waters end up giving people GI distress usually leading to diarrhea and sometimes vomiting. It’s not fun and any means to prevent the symptoms is welcome news.

But drinking cola? For me it seemed highly unlikely.

Yet the swimmer who swears by it also happens to be an Olympian and one of Canada’s better hopes for a medal.

Richard Weinberger, the 2012 bronze medalist in the Olympic 10K

You can read more about Richard and his quest – as well as his belief in cola – here:
Weinberger Predicting An “Epic” Olympic 10K Race In Rio de Janeiro

So, giving the swimmer the benefit of the doubt, I went in search of a possible mechanism behind his assertion. There were no clinical trials so any evidence he gave was purely personal and word of mouth. But that wasn’t a good enough reason to call it bunk. I wanted a mechanism to provide an explanation as to why it didn’t work – and also why people thought it might.

Then something strange happened. I came across an article from over 15 years ago. It was a rather obscure paper about killing E. coli on animal hides. You can see the abstract here:
The mechanism involved using phosphoric acid – just like the stuff found in cola – and mixing it with acidified salt water.

For me, this was an instant:

OSLO 20090612: A-ha med f.v. Paul Waaktaar-Savoy, Morten Harket og Magne Furuholmen inntok fredag Oslo for å markedsføre sitt nye album 'Foot of the mountain» som kommer i salg 15. juni. Foto: Berit Roald / SCANPIXA-HA! (if you don’t get this, ask your parents)

Reading the paper allowed me to see what could be happening in the gastrointestinal tract and why this cola trick might work. If you’re wondering, it goes something like this:

  1. Drink seawater – this is the only reason it works…freshwater won’t have any effect;
  2. Let it get acidified in the stomach – should be at least a few minutes if not more;
  3. Add phosphoric acid – drink the cola;
  4. Bow head for the gold medal – okay, this only applies to Weinberger.

I’m not saying this mechanism is actually occurring or that the technique works in the body. For that to happen, there would have to be clinical trials. Yet, as with many traditional remedies, this medical benchmark may never be reached.

For people like Weinberger and others, the answer comes down to whether they believe the mechanism. He does and if he stays safe, I’m happy for him. I admit I am skeptical. Yet, if I had known this idea when I was in Rio last year (and swallowed all that seawater) I might have given it a try.

As for my friend’s text message asking about cola and swimming, I know the people asking swim in the pool, not in the ocean. So in this case, the only answer is a very simple and emphatic:



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