The Germ Guy: Confessions of a Mercurial Microbiologist



What Brangelexit Can Tell Us About Antibiotic Resistance…

It was quite the week Two historic events happened over the last seven days. They were captured and shared by millions. However,  only one seemingly gained the attention they both deserved.

The first was one of the most important moments in our generation. It happened in New York and involved 193 countries all coming together to act on what might be the greatest threat in our time…

HLM Antimicrobial Resistance_Identifier

You may have heard about this meeting in the news. What you may not know is the result. It’s a political declaration of action to combat this rising threat to our health. You can read more about it here:

If you hadn’t heard about this meeting, I won’t hold it against you. Because the other incredible event stole away any momentum this might have seen. If you haven’t guessed it by now, it was the announcement that Brad Pitt and Angelina Jolie are…as my friend Sean Webb ingeniously coined…

jolie-pitt-cover-435x580Consciously Unmegacoupling

The news overshadowed any attempt to bring the plight of antibiotics into the spotlight. The Brangelexit, as it is now known, completely stole any chance the UN meeting had to increase awareness of the looming crisis. The declaration became little more than a small news story.

You might think I’m upset. I am. But I also know popular culture far outshines any scientific news, except perhaps…

plutodemotedPoor Pluto…

But as it’s the weekend, I didn’t want to go on some rant. Instead, I felt it best to find a positive from the announcement. As I searched my soul and my….

Plutonian Heart

I realized there was a link between the two events. In fact, I came to understand how the separation of these two mega-stars could actually provide perspective on antibiotic resistance. The feeling was so strong that I almost had to break into song. But, alas, that would not be good and so I decided instead on a different, poetic approach.

I present to you…

brangelinaThe End Of An Era May Save Another

 Woe has struck the land as Brangelina is no more;
The divorce papers have officially been put on file;
Now Hollywood is shaken to its innermost core;
The power couple’s love has turned to a rift most vile.

This tale of separation from a most valued friend;
Is happening in medicine and causing an ominous storm;
We are losing antibiotics upon which we so deeply depend;
Without action, living without them will soon be the norm.

Unlike Brad and Angie, there is hope for us still;
There are ways and means to prevent this great divide;
Now the UN has stepped in using its ceremonious quill;
Declaring the world is ready to act and abide.

We all have a role to play if we wish to avoid Brangelina’s fate;
Working in harmony we can beat antibiotic resistance before it’s too late.

Should Germs Accept The Blame For The Decline in Bar Soap Sales?

I received a note earlier this week about a disconcerting trend in hand hygiene. It seems the bar soaps are becoming less popular. While there are many reasons, one has to do with the fear of germs on the bars themselves. You can read the report here: Slippery Sales For Bar Soap.

While I had thought of writing a rant to refute the claims, I realized the long weekend might not be the best timing for a negative vent. So I sought to channel the emotion into something more constructive…and so I present a short, sweet, Shakespearean sonnet…

ivory-bar-soapThe Plight of The Slighted Soap Bar

One day I happened to browse upon the world wide web;
Hoping to read several stories in delight;
But a report from Mintel made my joy sharply ebb;
And I became more and more uptight.

The tale talked of bar soap, our old trusted friend;
But many apparently considered it a troublesome bane;
There were many a reason for this unwelcome trend;
Including a rather malicious and undeserving stain.

Many people now fear these bars are covered in germs;
They believe the risk of infection is high;
Yet a study – see here – reveals in no uncertain terms;
No threat to their health is nigh.

Sadly, I fear, we may not be able to turn back;
For it is hard to change behaviour in the midst of such meritless flak.


Science Communication, Isaac Asimov, and Creativity…

I am asked quite a number of questions when I’m on the road and as you might expect, most deal with germs. But every now and then, someone wonders exactly how to come up with inventive ways to communicate science.

One answer I like to give is…

isaac-asimovHeed the words of Issac Asimov

Dr. Asimov opened the door to widespread scientific communication through his wonderful writings. He also sparked imaginations worldwide bringing science closer to the individual.

During his tenure on this Earth, he wrote numerous essays on the topic of writing and creativity yet one of his most important for anyone interested in communicating science was written in 1959. It was for the United States Defense Advanced Research Projects Agency, better known as DARPA. It was simply titled…


The essay itself wasn’t released until 2014 and so I read it partly as an after thought as I was already well into my tenure as a science communicator. But as I read it, I found some parallels between his words and the work I was doing. Some of these passages included:

“A person willing to fly in the face of reason, authority, and common sense must be a person of considerable self-assurance. Since he occurs only rarely, he must seem eccentric (in at least that respect) to the rest of us. A person eccentric in one respect is often eccentric in others. 

Consequently, the person who is most likely to get new ideas is a person of good background in the field of interest and one who is unconventional in his habits. (To be a crackpot is not, however, enough in itself.)”

This represents the base for anyone interested in science communication. Rather than following standard routes, taking an unconventional – or, as my blog’s name suggests, mercurial – route can bring about both awareness and in some cases action on the part of the audience.

“My feeling is that as far as creativity is concerned, isolation is required. The creative person is, in any case, continually working at it. His mind is shuffling his information at all times, even when he is not conscious of it.”

When I am in the process of developing those parallels, I do it alone. I have tried numerous times to work with others but as Asimov says,

“The presence of others can only inhibit this process, since creation is embarrassing. For every new good idea you have, there are a hundred, ten thousand foolish ones, which you naturally do not care to display.”

It’s absolutely true. Most of my ideas simply do not fit the goal and are tossed aside. Though this may seem unproductive, as a researcher, it’s all part of the process. In the lab, the same trial and error is used to find the right hypothesis, the best experimental design, the most telling band or fluorescence marker, and of course, the most appropriate journal to publish the results.

All scientists go through these motions though I find few seem to realize how the actions of their vocation form the foundation for creativity. By giving oneself the chance to explore, that ability to find what works can arise.

I’ve only quoted a few passages from Asimov’s essay. I would truly recommend reading the entirety as it is a gripping read especially for anyone who has wanted to make a move towards the creative. He also uses the word sinecure in the most fascinating context.

You can find Dr. Asimov’s essay by clicking the link below:

Published for the First Time: a 1959 Essay by Isaac Asimov on Creativity

If you happen to be a science communicator, or are interested in giving it a try, let me know if the words in the essay ring true.



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:



Putting Perspective On Personal Fermentation

Hey everyone,

First off, it’s been an incredible few months since the release of The Germ Files. I’ve been touring all over Ontario and have been thrilled to meet hundreds of people all interested in our daily relationship with microbes. Also, I was pleasantly surprised to see a very kind review in the Washington Post.


You can read the entire piece here:

Over the course of the tour, one section seemed to gain interest with some of the audience members. It had to do with making fermented foods from microbes isolated from human fecal matter. The idea of finding new bacteria in the gut did have an expected effect…


monkees-nope(if you don’t know who these gents are, ask your grandparents)

But those feelings passed once I explained the lengthy process of isolating, purifying, and then testing a particular species. By the time fermentation happened, the bacterium had no direct links to the source an definitely would not have any related tastes. This practice is normal for any company wishing to use ‘human strains’ for their fermented foods and of course, probiotics.

However as in life there are always exceptions and just this past week, one seemingly has appeared.

bottled-instinctThe Order of Yoni Beer by Bottled Instinct

It’s well known beer is usually fermented with yeast. However, there are certain styles, such as the one pictured above, made with what is known as a sour mash. It’s particularly popular with home brewers though there are some larger companies using this technique to make a variety of choices. It’s also used to make certain American Whiskeys.

The key to a sour mash is the formation of lactic acid. To accomplish this, several species of bacteria have been used throughout the ages. One happens to be Lactobacillus acidophilus. The name may sound familiar because it is also a probiotic and as many on the tour have learned, is my favorite microbe.

jason-acidophilusMe and my L. acidophilus

The bacterium can also be found in a few places within the human body. The first is the same as I mentioned above. The company didn’t look there.

For those fluent in Hindi, the name of the beer, The Order of Yoni, gives away the other location. If you’re not up to speed on the Indian language, the word Yoni literally means the womb.

From a scientific perspective, the idea isn’t all that odd. After all, a sour mash made from isolates of Lactobacillus acidophilus acquired from a human female’s genitourinary microbiome may not seem all that bad. It might make for an interesting science or art project. After all, there have been such endeavours conducted in the past albeit not with this particular region of the body.

However, the company selling the product doesn’t quite explain it in the same way. Here’s a quote from their site:

“Using hi-tech of microbiology, we isolate, examine and prepare lactic acid bacteria from a unique woman. The bacteria, lactobacillus, transfer woman’s features, allure, grace, glamour, and her instincts into beers and other products, turning them into dance with lovely goddess.”

Needless to say…

carrie-wth(If you don’t know who this is, ask your parents)

As you might expect from the description and the model, this venture is all about trying to bottle the essence of beauty and provide it in a relatively easy to digest format. The company goes even further to name the person from whom the sample will be taken…a model named Alexandra Brendlova. If you don’t know who she is, here’s a promotional photo.


While this may be enough to convince people to give this a try, from a scientific perspective, the only place you’re going to feel anything is your wallet.

If you go deeper into the site, the company explains the process of isolating this unique Lactobacillus acidophilus for brewing. It’s no different than trying to isolate a bacterium from that other region. The samples are cultured, and the bacteria are isolated, and then grown until they reach the right levels to be used in the first stages of fermentation. This ensures safety but also takes away any links the species may have had to the owner.

There is one bright side to this venture. This concept shows just how popular microbes have become over the last decade. It really makes me wanna…

5sos(If you don’t know who these guys are, ask your kids)

While this particular product may not provide anything more than an intriguing sour mash beer, the interest from the media and those actually investing in the company reveals this may be the beginning of mainstream human microbial artisanal gastronomy.

If you are interested in going this route, I’d love to hear about it. Just be sure not to overstate the benefits. Though bacteria may come from a specific individual or type of person, don’t expect to transfer their outwardly qualities. A person may gain health benefits and perhaps help to change several biological parameters. But in terms of features, allure, grace, and glamour, no amount of Lactobacillus or any other microbe for that matter is going to help.

If this was the case, fecal transplantation would be a far more common practice.



Would love to hear your thoughts…









A Trifecta Coda To Antibiotic Awareness Week

Hey everyone…

I know it’s been some time since I wrote here. For more on why, check out my front page.

Last week was a special time for those working in public health.  It was the first…


After 70 years of knowing bacteria can become resistant to these life-saving drugs, the world has taken notice.  You may have seen and heard headlines in the media over the last week discussing antibiotics. The situation has become a crisis as we face what is known as the post-antibiotic era.

But what exactly does that mean? Perhaps this might help:


This is just in the United States – worldwide, the number is far greater.

The statistics are frightening and the risk for troubles are growing.  But while the message about antibiotic resistance spreads, some of the more valuable information has been left unsaid.

Now that Antibiotic Awareness Week is over, I wanted to add a coda to the event. I wanted to bring attention to the issue by going into the science of the issue and show some of the latest work describing just how resistance comes about, what we can do in the present, and a look to the future.

popsci-resistanceThe Complexity of Antibiotic Resistance

First, my Popular Science column explores how antibiotic resistance comes about. It’s all about a word used quite often in ecology:  fitness.  When a bacterium comes into contact with an antibiotic, it may die but it may also find a way to survive. Depending on the drug, the fitness differs, even for the same bacterium.  This reveals how dynamic resistance is as a whole and why it is so difficult to prevent.  After all, you’re looking for a needle in a haystack.

mechanismThe Ways Antimicrobial Peptides can kill bacteria

My Huffington Post Canada column takes a different look at the problem by looking forward to the future. Because resistance to antibiotics is so hard to tackle, the best way to approach it is to look for alternative measures.  One of the best options is called an antimicrobial peptide, or AMP.

These molecules are simple in design and extremely effective at killing bacteria. The supply could be endless as almost every species on Earth produces them. All we need to do is go hunting for them and then test them in the lab. Though it may take some time, AMPs may be the answer to antibiotics and may one day become the treatment of choice.

Finally, I wanted to take a completely different perspective on antibiotic resistance not seen in the news. For this, I teamed up with two great video experts, Jay Trout and Sean Webb. Together, we put a short 2:22 video together on where you can find antibiotic resistance and what you can do to help prevent the post-antibiotic era.

As you’ll see, there are three easy ways you can make a difference.  After all, we all play a role in stalling the approach of the post-antibiotic era.  We can all do our part.

For those wondering, the video is in Standard Definition so anyone with a slow internet stream can still watch it. If you are looking for an HD version, just let me know.

Antibiotic resistance will continue to be a problem for a very long time. But knowing the trifecta past, present, and future will ultimately help us to achieve the goals of Antibiotic Awareness Week. We cannot lose our ability to use antibiotics…at least not yet.  Let’s make sure we are all helping to make a difference.

As always, would love to know your thoughts.



A Germ Wars Webchat…


The webchat went extremely well!  A special ‘Thank You’ to participant “Diane G.” for sharing her longtime support.  People like her give me even more reason to continue what I am doing.  If you missed it, you can read the text here:

My interview with CBC Ottawa Morning is now up.  You can listen to it here:

Tuesday’s story on kids and germs is now up.  Watch it here:


Hi everyone,

It’s been a while since I’ve posted here although I hope you have all been enjoying my articles with the Huffington Post.  It continues to be a blast and I am eternally grateful for all the positive feedback I have received.

This week, CBC Ottawa has been running a series called Germ Wars and the great David Gerow took me on a wild journey around Ottawa where we went on the hunt for germs.

The series started yesterday and even featured a cool Germ Quiz which has garnered some very interesting comments.  The series continued today with a discussion on kids and germs and will conclude tomorrow with a story on pets and germs.

Now here’s the fun part…

Tomorrow, Wednesday October 24, at Noon EDT, I’ll be taking questions from the public during a one hour webchat.  You can head to the site then and ask anything relating to germs, hygiene and health.  The link is:

I hope you can find some time to get involved in the discussion.  Based on what I have already heard from people who have seen the series and taken the quiz, it will be a lively time.

Looking forward to seeing you there!

Happy #handhygiene Day!

It’s May 5th and the world is celebrating!

(yes, it’s Cinco de Mayo, but it’s also…)


Or, as I like to call it:  #handhygiene Day!

The original reason for this day was to help prevent infections in health care activities worldwide.  While others and myself have expanded the scope to include any hand hygiene activities, the WHO still keeps its focus on making some of the worst offenders…doctors and other health care professionals…get with the message and start to help rather than hinder health.

With that, here are a few ways to learn a little more about the importance of #handhygiene and to engage others in discussion, debate and of course, silly photo sharing!

1. Press Release
Here’s a great press release that offers a little more insight into why Clean Your Hands Day exists and perhaps a few pieces of data that some might not want to know.

Click for more

2. Twitter Feed
If you take a peek to the right of this page, you’ll notice my twitter feed.  I’m working to share the seven important points on #handhygiene.  There are some fundamentals that simply need to be known to stay safe anywhere.  I hope you check out my feed – or just click here – and enjoy

3. Share YOUR story!
I know that each and every one of us has a story to tell about how #handhygiene has helped us in one way or another.  I have several although perhaps my favorite occurred about 15 years ago in a land quite far away:

It was 1997 and I was deep in the Southern regions of Turkey on a tour tracing back the history of our civilization (hey, I’m kinda into that stuff!).  The tour bus came to a stop at a convenience stand that acted as a grocery, restaurant and pit stop.  After picking up some lokum in the grocery and some elma chai in the resto, I went for the pit stop.  Let’s just say that our concept of a toilet is different there.

(they lose a dimension it seems).

It was one of my first times working with a 2-D toilet and it didn’t go well.  I won’t get into details but I was thankful that there was a hose running nearby.

I had ‘finished my business’ I noticed that there was no sink.  When I ventured back to the stand, I asked for soap and water (sabun ve su) and was met with a curious glance.  A moment later, the nice gentleman revealed a bottle with a yellow liquid inside.  He presented it to my nose and I noticed that it was a lemon scented perfume.  It was a nice thought but it wasn’t about to help.

Back when I was a child, my mother had come up with a great formulation to stop the the spread of infections.  It was a combination of 70% rubbing alcohol and 10% glycerin.  The formulation had been used for decades ‘under the radar’ as a means to prevent infections in the field.  For me, the mixture had been a hand saver on many occasions throughout my school and university years and it was going to be nearby during any trip.

So, with a nod to the gentleman, I went back to the bus, found my backpack and took out a small bottle containing the mixture.  That moment of knowing that you are safe is unlike any other.  At that moment, I put the that bottle in my pant pocket and decided that for as long as I live, I’ll never be unprepared again.

It’s my prop de vivre!🙂

Okay, now it’s your turn!  Share your story on how #handhygiene has helped you stay safe in the comment box below and I’ll share it with the rest of the Twitterverse!

4. Share your photo
Everyone loves a great photo!  Now it’s your turn to share your #handhygiene photo with the world.

  1. Take a photo of handwashing, sanitizer use, teaching your kids, teaching your parents, and so on.  Show your passion for staying clean!
  2. Share it on the social media platform of your choice.
  3. Tell me about it and I’ll post it here.
  4. Have fun!!!

All right, it’s time for me to sign off and spread the sanitizer!  Have a fantastic #handhygiene day and I look forward to reading your stories and seeing your photos.

Happy #handhygiene Day to you all!

Tomorrow is #handhygiene day!!!

It’s that time of the year again and I couldn’t be happier.

Two years ago, I started #handhygiene in support of the World Health Organization’s SAVE LIVES: Clean Your Hands campaign to improve hand hygiene in health care worldwide.

Since then, #handhygiene has grown to include every aspect of health and hygiene from the sublime to the absurd.  The hashtag is now listed with the Healthcare Hashtag Project and continues to move ahead without any sign of slowing.

Ultimately, I have to thank people such as Barry Colpitts (@Colpittsb), Patrick Boshell (@DebMedProgram & @Deb_Canada), Louise Taillon (@EnviroWeezy), the Canadian Patient Safety Institute (@Patient_Safety), Michelle Forman (@APHLNews), Lana Targett (@LanaTargett) and our very own handwashing superhero, the Mighty Bubble (@Mighty_Bubble) for making #handhygiene work every day of the year.

There have been hundreds of others who have contributed over the years (some you can see above) and I am grateful to each and every one of them for finding room for #handhygiene somewhere in the 140 characters allowed (it’s not easy!).

Finally, I am truly grateful to the people who inspired #handhygiene in the first place.

World Health Organization.  

To Christy and Sari, I am honoured that you’ve taken the time to notice the hashtag, the work that we are all doing and to share your plans and materials with The Germ Guy.

Now for this year’s #handhygiene day…

I’ll be sending out messages from the WHO pointing out why we celebrate this day and why we need to keep focusing on how to keep our patients safe.  I’ll be posting to Twitter, Facebook and of course here on my blog.  I hope that you take the time to read, share, retweet and comment.

One final note – if you have any personal stories, concerns or ideas, be sure to put them here.  I’ll be sharing them with the people at the WHO in the hopes that they will continue to keep record of the realities that exist and how we can best move forward in safety, health and of course, #handhygiene.

Until tomorrow…

Create a free website or blog at

Up ↑

%d bloggers like this: