The Germ Guy: Confessions of a Mercurial Microbiologist



Mathematics and the Zombie Apocalypse

When it comes to cultural curiosities, few compare to the popularity of zombies. These undead creatures, born out of Haitian mysticism, have become a worldwide phenomenon. Around the world, cities host thousands of people for zombie walks to celebrate these rather grotesque creatures with a hunger for brains. Books and movies have been made about them and a few years back, the CDC developed a zombie preparedness plan for the so-called “zombie apocalypse”.


(granted it was tongue-in-cheek)

But while zombie-based research may seem to fall in the realms of microbiology (zombie virus), physics (zombie radiation), or survivalism, the one area gaining the most ground is epidemiology, better known as the study of disease spread.

The tools of this branch of science are mainly mathematical and have helped to understand how a variety of infections can spread. But when it comes to total annihilation, nothing beats the zombie apocalypse as a model. This fictitious event can provide the perfect base for complex equations to determine how a pathogen might spread. To wit, scientific articles and even academic books have been written on the subject.

But now it seems zombies may be used as a learning tool for mathematics. In a recent study, a group of researchers make the case for using popular culture as a base for scientific learning. They expressed their views in a paper, which you can read here:

Equations of the End: Teaching Mathematical Modeling Using the Zombie Apocalypse

As the authors state in the conclusion, the approach:

“brings the teaching of infectious disease modeling into line with how biology, epidemiology, and public health are often taught, with subject-matter expertise being acquired after, or alongside, general methodological sophistication, rather than acting as an impediment to it.”

Granted, that’s a pretty long sentence to justify their perspective. Yet, the gist is pretty common to anyone performing science communication. If you want to make a rather dry subject seem interesting, throw in some pop culture.

The beautiful part about this direction is the ability to make up the details as you go along. Unlike some of those pandemic movies, which are usually subject to much scientific criticising, being accurate to the specifics isn’t needed; zombies are fiction.

So, if you want to have some fun learning about how it might end, take a look at the paper and keep your eyes out for courses. Much like zombie-based activities, I’m sure the learning opportunities will be popping up everywhere fairly soon.

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…









Antibiotic Resistance and Rethinking The Name “Superbug”

As some of you may know, every month, I have the honour of being a guest on the Ward and Al Show on SiriusXM Canada Talks (Channel 167). For the hour, I get to talk about the wonderful world of science with the hosts…


Ward Anderson and Alison Dore

I adore them because they have an incredible interest in science but more importantly, how to make the strange world of the lab come alive in the public realm.

We normally talk about headlines of the day and sure enough, last Monday, the topic turned to antibiotic resistance. It’s been featured quite often over the last few weeks as a crisis looms over our ability to fight infectious disease.  We may even enter what is known as…


The Post-Antibiotic Era.

Almost sounds like something from a comic book, doesn’t it?  Well, when the subject turned to what exactly antibiotic resistance looks like, there was no better place to turn than the comic book world.  Or, in this case, movie trailer.

Last week, the new Batman vs Superman trailer was unveiled and it is quite the experience. But there’s an interesting scene contained within the three minutes that has many a fan talking. Head to about 2:20 and watch for the next twenty seconds.

The monster is known as Doomsday and has the potential to wipe out an entire city block with one burst of incredible molecular energy.  As you can see in the trailer, he’s pretty good at it and can cause some major devastation. For Batman, this appears to be a certain demise.


He lives thanks to the introduction of an even more powerful shield donned by none other than Wonder Woman. Thanks to her, the Caped Crusader is saved and the world is introduced to yet another superhero.  Even more intriguing is her appearance was not chaperoned by either Batman or Superman.  She somehow appeared out of nowhere and ended up saving the day…at least for the Dark Knight.

It’s a pretty fun scene although at first glance, this seems to have little to do with antibiotic resistance.  Let me explain…

First off, antibiotics, while chemical in nature, are very similar to that energy burst from Doomsday.  All targets, bacteria and human cells are affected and many end up getting wiped out (yes, even our human cells can fall victim).  Not to mention, the landscape after an antibiotic treatment is devastated.  For a sensitive bacterium in the midst of the onslaught, death is a certainty. As Martha Stewart might say…

and-thats-a-good-thing(Yes, I went there)

Now, if a bacterium somehow develops resistance to an antibiotic, it has in effect picked up that shield and can survive the attack.  The shield could be a barrier or in some cases it could be a mechanism to break down the molecular energy rendering the antibiotic useless.  Either way, the carrier of the shield – and in many cases, those in the immediate vicinity – are saved and given the chance to fight another day.

As we all know, leaving an embittered entity in the middle of a wasteland can lead to even more troubles. For anyone suffering from an antibiotic resistant infection, they know this well. The bacteria grow without hesitation and in many cases end up producing even greater troubles thanks to toxins and other attacking chemicals.

Because of their ability to resist and eventually cause troubles, we tend to call these bacteria…



In light of this particular trailer, though, I wonder if we may need to re-examine this term.

Think about this:  in the midst of Doomsday’s energy, Superman would have been just fine. He could handle the burst in the same way he seems to be relatively invincible.  Granted, there are some things that could hurt and possibly kill him (Kryptonite, anyone?) but in general, he’s pretty much unstoppable.

Batman, on the other hand, was a sitting duck. Without any type of resistance, he was surely a goner.  But thanks to the arrival of the Amazing Amazon, he was given a chance to embrace the protection. Of course, if she didn’t have that shield, she would have joined her human counterpart as a victim rather than a survivor.

If you look at antibiotic resistant bacteria, they are nothing like Superman.  Even if they could resist to all antibiotics – we call them pan resistant – they most likely can be killed with good ol’ fashioned soap and water. They are physically feeble and incredibly dependent on water, food, and a welcoming environment.  They are not super by any means. They simply have the weapons and defenses to keep them alive in the harshest climes. So why call them Superbugs?

Okay, I know it’s not all that important what they are called.  It’s just a fancy name for a particular group of bacteria. But in light of what we now know about their biology, biochemistry, and activities in various environments, including development or acquisition of resistance, perhaps it’s time for a change in perspective and in name.

Of course, choosing a new moniker may not be easy.  If we adopt the same superlative as the female shield bearer, we end up with…


Not to mention, there already is a wonder bug out there in the form of a car with a magical horn.  If you can remember…


…you are definitely over forty.

While “Wonderbugs” may not be the best choice to call antibiotic-resistant bacteria, we still need to examine a different nickname.

I think a better option would be to use a term based on their characteristics.  Let’s focus on the reality and leave out the superlatives. We don’t have to be academic either as there’s apparently no harm in creativity.  After all, we are in a world where the Son of Yeezus is called Saint (if you don’t know what that means, you are probably over forty).  I am sure we can find a good balance between science and the public.

So, with that in mind, let’s see if we can come up with a better name for antibiotic resistant bacteria than “Superbugs.” If we find one we all enjoy, we might even make it spread like a virus (which by the way is not affected by antibiotics) and become adopted in the public.

I’ll start by suggesting what I would love these bacteria to be called:



(Antibiotic Resistant Microbes Of Relevance)

The first part is self-explanatory. But the second offers perspective on the importance of antibiotic resistance in our lives. After all, resistance is rampant in the environment but many of these species with shields are harmless to us and pose no threat to our health or medicine.  All together, it makes for a very good and scientifically accurate name to reflect the mechanism of antibiotic resistance.  I’m sure even superheroes would love the term.

Now it’s your turn. What is your suggestion to replace “Superbugs”?

Hope to hear your thoughts…

What Adele Can Teach Us About The Flu Vaccine

If you follow popular music, then you’ve no doubt heard about…



This incredible songstress has been smashing records with her new album, simply entitled, 25. She has taken the music industry by storm and has reinvigorated the music scene. So much so, she had an entire television special devoted to her entitled, “Live in London.”

During her performance, she sang one of her most beloved songs, “Someone Like You.”

Most people in the audience knew the song and many joined in if only quietly.  But then, something happened at about 1:35 in the song.  She changed the melody, singing in a very different fashion than expected.

The audience sat back quietly listening, learning, and eventually figuring out the new direction.  By the end of the song, the people were back, singing with her, matching the new notes perfectly generating a perfect moment for everyone there and watching from afar.

As I sat watching, I was taken by the experience and immediately thought to another important part of our lives…


The Immune System

Much like the audience, our immune systems are forced to deal with something altogether new and unexpected such as a novel strain of the flu.  Eventually, though, our defense forces develop a response and evolve to the changed environment.

The only difference is the time it takes to adapt.  As you can see, the audience needed only a few minutes.  Our bodies need much longer, up to three weeks.  During that time, we experience cellular confusion, viral analysis, and attempts to respond which manifest in the form of symptoms. Yes, those coughs, sniffles, aches and pains are simply due to our bodies trying to figure out how to deal with the unknown or at least changed entity.

Much like anyone trying to learn a song, immunity needs practice to achieve the right match.  This can be difficult without some type of guide.  All one has to do is ask musicians about the trials and errors of figuring out an entire piece of music from scratch only using their ears.  It’s a painstaking task with a variety of symptoms – usually psychological – attached to it.  For immunity to achieve the same result, our bodies have to undergo the same tribulations.

But there is a way to reduce the time and effort needed to gain the ability to learn.  For a musician, this comes in the form of sheet music and/or prior recordings. For our immune systems, it’s…



A vaccine is for the most part, an easy method of training the immune system to adapt to a particular pathogen.  It’s essentially a biological form of sheet music or recording allowing our immunity to adapt to the invader and learn how to react.

Normally, only one or a few shots are needed to accomplish the task. But there is one case where a single shot is simply not good enough. It’s the influenza virus or, the flu.

As I said in my book The Germ Code, this virus is the master of evolution and is continually changing.  Our immune systems have to figure out how to react to these changes.  But the change is minimal. If we have already experienced a similar version of the virus, we can fight while we adapt. If we have had no previous exposure, the time it takes to react may be insufferable.

Take Adele’s song change.  The audience already knew 95% of the music and lyrics so the minor change allowed for a rapid adaptation.  If she had sung something completely unknown, however, she would have been met with silence.  There simply would not have been enough time to evolve and adapt to the new combination of notes and words.

The same exists for influenza. If we have already seen most of the virus in the form of infection or vaccination, any subsequent infection may end up being mild.  The more we are infected – or preferably vaccinated – the better trained our bodies will be against the virus.  It’s why getting a shot every year can be helpful even if you never come into contact with the flu.

Of course, there are some times when a vaccine may not match the virus exactly.  We saw that last year when the formulation missed one of the targets.  But…


That was only one of three strains (the first one). The others were gave the expected levels of protection across all ages. This meant there was still a good reason to get the shot.

I appreciate this may not be entirely convincing as the numbers are far less than what people expect from a vaccine: 100%.  Yet, when it comes to the flu, the immune system can use all the help it can get.  Even if the protection isn’t perfect, by having that training, when the virus does show up, our immune systems can adapt more quickly and help to reduce the severity of symptoms.  Considering the impact of a full blown infection while our immune systems try to adapt, it may be well worth getting the shot, even if it is a partial miss.

As always, I would love to know 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.



The Science Behind Mom’s Cold and Flu Remedies…

Hey everyone,

It has been quite the week for good germs.

First, a story coming out of Australia revealed how the use of one particular probiotic strain, Lactobacillus rhamnosus, can help to alleviate peanut allergies.  Although the paper is not open access, you can read the summary of the study by clicking on the photo/link below.

untitled (2)

The other story making headlines was the impact of probiotics on mental health. For the last decade, trials have shown the benefit of good germs for the mind. The can help keep the mind calm as well as reduce stress and anxiety levels.  Now it seems Canadian researchers are performing clinical trials to determine the benefit of taking probiotics instead of prozac.

I spoke on this earlier in January with the CBC and the producer it was very well received. Some have asked for a link to the broadcast and I’m happy to say you can hear the segment below.


It’s such a pleasure to see the benefit of good germs in the news but as we all know, there are microbes that cause us misery including cold and flu viruses.  Hygiene and social distancing (stay home when sick) are great ways to prevent illness.  Yet, at one time or another, most of us find ourselves victim to the sniffles, coughs, aches and pains.

When we get sick, a trip to the drug store is the usual course of action. But there are more natural ways to fight the bugs and regain our health. Many are traditional in nature and they differ depending on one’s background.  These remedies are homegrown and range from the reasonable to the extreme – mustard plaster anyone?  But one thing is for sure: most of them work.

On Friday, I had the wonderful opportunity to discuss these remedies with the radio program, Ontario Today. The goal was to reveal scientifically how these remedies worked and why they are sometimes as good as modern medicine.

For the next two hours – on air and online – I was treated to dozens of examples originating from all over the world.  Although I’d heard of many in the past, some were quite simply out of this world. Yet, they all worked and the science could prove why.

Essentially, a home remedy should accomplish at least one of three goals.

1. Reduce the level of inflammation, which is a consequence of infection

2. Improve blood flow to shift the body from lethargy to action 

3. Utilize antimicrobial properties contained in the remedies to kill viruses  

As each one was brought up, the science became clear either through mention of the ingredients or through the overall results.  All I had to do was classify them and when possible within time constraints, provide a mechanism.

If you want to check out the discussion, you can head to the Ontario Today website. Both the radio and online portions are there.


It was such a fantastic time for me because of the two-way conversation between scientists. Each caller was a scientist (or a representative of one, usually their mothers or grandmothers).  We had a collaborative conversation.  Then there was the passion expressed by each contributor. The experience was akin to a scientific conference where researchers are eager to share their findings with the rest of the community.

I’ll end by asking if you have any old style remedies you want to share. If so, put it in the comment section below. I’m sure people would love to hear how you go about fighting the cold and the flu.

I know I would…

Exploring Self-Actualization (and Germs)

Over the years, I have been fortunate enough to have had the ability to share my views with the public through the media.  Yet even more fulfilling have been the one on one interactions with people who approach me to ask me questions about germs and our relationship with them.

But one question recently offered me an opportunity to explore our bond with germs on a deeper scale.  It was a short one with an even shorter answer but opened up a discussion I never thought I would have.

The question:  “Why do you want us to have a better relationship with germs?”

My answer: “Self-actualization.”

The quizzical look on the person’s face revealed the expectation of a different response but as we ventured further into the topic, a different perspective was unveiled.

Self-actualization is a relatively new term in the human lexicon, based on a branch of philosophy called “Organicism”, which is still best outlined in a text from 1903 called L’hérédité et les grands problèmes de la biologie générale. The essence of this theory was fairly simple yet the implications were profound:

“…life, the form of the body, the properties and characters of its diverse parts, as resulting from the reciprocal play or struggle of all its elements, cells, fibres, tissues, organs, which act the one on the other, modify one the other, allot among themselves each its place and part, and lead all together to the final result, giving thus the appearance of a consensus, or a pre-established harmony, where in reality there is nothing but the result of independent phenomena.”

While “organicism” was enough to placate a number of theorists, for researchers such as neuropsychologist, Kurt Goldstein and psychologist Abraham Maslow, this definition wasn’t enough.  An individual had to be aware of how all the different parts worked together to bring about a healthier self…or as they coined it, self-actualization.

Both researchers set out on a path to identify just how we could be more self-actualized. Goldstein took a medical approach focusing on language while Maslow took a humanistic one.  Both, however, came up with similar conclusions:

In order to have a better life, we must first identify the individual parts that
make up our lives and then figure out how these parts work together.
More importantly, there is a need to understand whether the relationship
can be changed by outside influences.

From a biological perspective, Maslow offered a rather intriguing look at how self-actualization works in our daily lives.  His target was not some abstract component of behaviour but rather one that has become all the rage in the health world:  Vitamin D.

Back in 1973, in his book, The Farther Reaches of Human Nature, Maslow noted that Vitamin D is a needed nutritional supplement to keep babies from catching colds and suffering other illnesses.  Deprivation not surprisingly led to sickness.  Replacing the vitamin with a poor surrogate led to the same problem.  Essentially, in order to live a happy and healthy life, one needed to ensure that the body (and the mind) were supplied with proper supplements and not subjected to either deprivation or an unsuitable replacement.

In essence, by changing one component of a healthy life in a negative way, the entire existence suffers.

Up until a few decades ago, this theory may have had little in common with the world of germs.  After all, for most of history, germs have been our enemies.  But with the identification of good germs, probiotics, and the microbiome, our view of the microbial world has shifted.  Only a small percentage are truly enemies while the majority are either beneficial or even essential to a healthy life.

Today, we know that health is directly related to germs.  The makeup of our gut microbiota can influence a number of different health factors, from body weight, to management of chronic conditions to psychological state.  While we continue to learn from researchers, the trend is unmistakable.  Much like Vitamin D, germs are a necessary part of our existence and if we are deprived of them or worse, given improper surrogates, our happiness and health is in jeopardy.

But self-actualization is more than just knowing, it is also acting.  No matter how much you might know about Vitamin D, if you don’t take the supplement or get some sunlight, the knowledge will do you no good.  The same exists with germs.

Unfortunately, for most people, that is a problem as there is almost no availability of information on how to keep a good rapport with our microbial counterparts (although The Germ Code is available for pre-sale).  This gap leaves many with questions, concerns and in some cases health issues that might be managed or resolved by simply changing the relationship.

As The Germ Guy, I try to fill that gap the best way I can. Promoting the use of good germs and means to avoid the bad ones is only the beginning. Bringing light to new revelations in the scientific literature increases awareness; highlighting new trends helps individuals decide on beneficial actions; and linking germs to some of our most popular cultural phenomena brings the microbial world closer to our reality.  It’s all in the name of helping self-actualization and bringing about a happier and healthier life.

The talk led to some thinking on the part of the asker and ended with another form of self-actualization.  This person, who is an expert in a different field of science, decided to start an expert blog. The goal, like mine, would be to help people self-actualize in that specific scientific realm.  I was thrilled.

I also learned one other aspect of self-actualization that I hadn’t given much thought.  By acting on our own motivation and striving to better one’s life (and perhaps the world’s), we can also inspire others to do the same.  While my work will always focus on germs, I am happy to know that the impact reaches far beyond the microbiome and into people’s motivation.  That in itself is perhaps the highest honour.

I would love to hear your thoughts.

A Germy View of the Situation in Egypt

Like millions of others worldwide, I’ve been paying close attention to the events happening in Egypt.  For the last two and a half years, the country has experienced what can be best described as a sociopolitical roller coaster ride.  The 2011 Arab Spring to oust Hosni Mubarak was regarded as one of the most powerful public movements yet paled in comparison to the current unprecedented gatherings to protest the now-deposed President, Mohamed Morsi.  Whatever your political view, you cannot argue that what has happened in this small corner of Africa has been historical.

Yet, while this movement on a human scale may seem rare if not unique, the same type of struggle often occurs in the microbial world, particularly in the human gut.

When happy and healthy, the gastrointestinal tract is colonized with a combination of helpful microbes that work together to help digest food, balance the immune system and even send signals to the brain that all is good.  Yet, when another type of microbe ventures in, such as norovirus, Salmonella or C. difficile, a struggle ensues.  The outcome, much like political strife, can happen in one of three ways.

In the case of norovirus, as anyone who has suffered this infection knows, the result is akin to a pillage, sending the gut and the body politic into turmoil within hours.  The virus metaphorically scorches the gut leaving it almost uninhabitable.  After the virus has completed its horrific task, usually 48 to 72 hours, it leaves the body in search of its next conquest.  The gut, however, cannot heal as quickly and may need weeks if not months to heal, recolonize with good bacteria and eventually return to a content state.

For Salmonella, the battle is like an insurgence that goes back and forth until one side wins.  If the pathogen is strong enough and in high enough numbers, the good bacteria are overwhelmed, being killed off or ousted from the body as diarrhea.  The gut countryside becomes a Salmonella state ensuring that the microbes are fed well and thrive.  Eventually, as the body recognizes the problem and learns to fight the pathogen, a process that usually takes no more than a few weeks, the Salmonella are beaten down by both the immune system and any newly introduced fighters, such as antibiotics and/or probiotics and eventually cast out of the body.  The healing process takes some time, perhaps weeks, but because the landscape wasn’t entirely decimated, there can be a rapid return to normal life.

Opportunism is the best way to describe C. difficile. Normally, this bacterium is harmless and cannot establish any kind of presence in the gut, even though we are exposed to it fairly regularly in the community.  Yet, when a battle in the gut has taken place, such as an infection followed by antibiotics, there is a chance that there will be no clear winner – the gut will be left relatively bare.  C. difficile can take hold of this opportunity and start to form its own colonies.  However, much like an opportunistic dictator who takes over after a war, the bacteria makes its own decrees regardless of the state of the country.

The bacterium releases a toxin that can kill anything in its path.  Over time, it forms its own castles in the gut, known as pseudomembranes.  Also, due to the lack of a proper connection with the body, it renders the entire person in a state of illness.  Diarrhea is common, pain can be at times unbearable and eventually, in the weak, the only salvation is death.

What makes C. difficile so problematic is that once it has laid down its foundations, it is very difficult to remove.  No matter what kind of fight might ensue, the bacterium fights until the bitter end and will not give up its reign until it has been killed off completely.  While possible, it’s not easy on the patient and can lead to even more troubles down the line.

As for Egypt, the situation is different; the changes that have occurred have been for the most part non-violent and mediated by the people.  While there have been deaths and other crimes against humanity recorded, for the most part, the process has been peaceful. In a microbial sense, the people of Egypt are akin to probiotic bacteria in the gut.

Individuals want to have a healthy and prosperous country and will do what they can to preserve a beneficial state.  In 2011, these probiotic people amassed in Tahrir Square to protest years of unhappiness under Mubarak.  In 2012, they allowed another type of bacterium to enter the fold – Morsi – along with his supporters.  However, much like what happens in cases of irritable bowel disease (IBD), the presence of these new players was less than beneficial, causing a form of dysbiosis.  The body economy suffered, the psychological state worsened and relationships with other bodies became sour.

But as seen in many cases where IBD is managed and resolved, the public version of probiotics once again came to the rescue.  A new and even more powerful rise occurred.  Through their protest, a signal was sent to the immune system – the military – to do what is right and attempt to restore balance.  While there may soon be calm again, much like the medical state, the political state is far from being at peace and the people may once again come out into the streets if displeasure occurs.

The world is a continually dynamic and there are so many ways that our social, political, economic and even interpersonal worlds shift and change over time.  But the Earth is in many ways no different than each and every human body.  One can take a closer look inside at the microbiome, the immune system, the nervous system, the endocrine system and others to not only identify ways to relate, but also to see how outcomes may turn out.

In the case of Egypt, while resolution may be a long time away, I am sure that as long as the probiotic people are out in force, the entire country will stay in at least some kind of balance – as long as they don’t have to worry about another norovirus, Salmonella, or C. difficile.

As always, I would love to know your thoughts and whether you know of other germy models for sociopolitical events.

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!

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