The Germ Guy: Confessions of a Mercurial Microbiologist



Do You Really Need An Antibiotic?

This week has been filled with controversy. In that vein, I feel it’s a good time to say something equally controversial:

Sometimes the best antibiotic prescription
is no prescription at all.

Okay, if you happen to be in public health, especially in Canada, this might not seem all that troublesome. After all, it’s been a mantra in the medical community for years. Yet, considering we still hear about the abuse and misuse of these life-saving drugs, the guidance hasn’t been accepted universally.

One of the reasons for the lack of compliance is based on a statement I hear quite often when I’m out in the public realm. Maybe you have heard it – or said it – at one time or another:

Prove to me I don’t need an antibiotic.

Admittedly, it’s a difficult request. But over the last few years, researchers have been exploring whether a person can deal with a bacterial infection without the use of antibiotics. The answer is yes but finding a way to show this to the public has been a real challenge. Usually, the information is hidden in statistics, which can be subject to skepticism.

However, I came across something that might demonstrate why forgoing an antibiotic may be worthwhile. It looks something like this…

 (Kinda cool, eh?)

What you’re looking at is a figure that comes from a paper entitled, Symptom response to antibiotic prescribing strategies in acute sore throat in adults: the DESCARTE prospective cohort study in UK general practice. You can click on the title to read the paper.

As you can guess from the graph above and the title of the paper, the researchers examined the progression of the traditional sore throat based on symptoms. They looked at 1512 people who had suffered the illness. The symptom information then was matched with the treatment the individuals received.

  • Some had no antibiotics (the blue);
  • Some had a regular antibiotic prescription (the red);
  • Some had what is known as a delayed antibiotics (green).

Delayed antibiotics is a recent trend going around in which a patient is asked to wait a few days after an initial visit to determine if the infection goes away. This is a great way to determine if the infection is bacterial and may need antibiotics, or viral, in which case antibiotics are useless. This approach also allows the body to fight the infection few days. There’s a good reason for this:

The immune system can handle
many infections on its own.

Based on all the results, the addition of antibiotics resulted in an observed reduction in the length of the worst symptoms. But the extent was far less than anyone might have believed. In fact, once all the numbers were crunched, the benefit ended up being equivalent to a grand total of…

One day.

That’s it. Twenty-four hours of lessened symptoms. Nothing more.

The researchers did happen to point out that those who didn’t take antibiotics had a harder time dealing with the infection throughout the period. But in the end, they recovered just as well as those who had taken the antibiotics.

The results of this study may help add credence to the mantra, but that doesn’t mean forgoing antibiotics is valid for every infection. Just recently, I came across an individual who had a sore throat and decided not to take antibiotics. The person lasted a week before caving in to the pain. The bacterial infection was more troublesome and the immune system needed a boost.

If you are wondering what the best option might be should your throat start to scratch, your urinary tract start to burn, or your eyes begin to turn red and water, let me be perfectly clear:

I can’t tell you.

This is a decision that only can be made between you and your doctor.

What I will advise is that when you do feel those troubles and you make that appointment, don’t be quick to ask for a prescription. Your doctor may want perform some tests first to find out what might be causing the troubles. You may be asked to wait and see if your immune system can pull through. Or, there may be ample evidence to make the prescription immediately.

Just remember, if you are given a prescription and fill it, you need to stick with it until the end, even if you feel better. This way you can be sure that you are clearing your body of the infection and reducing the chances for recurrence down the road.

Finally, I’m curious about the use of antibiotics. So, let me ask a relatively simple question I hope many of you won’t mind answering:

When was your last antibiotic prescription?



Solving World Hunger With Bacteria…

Back in 1999, a movie came out that revolutionized science fiction and led to one of the most iconic lines in movie history…

(Welcome To The Real World…)

If you haven’t seen the film, I suggest you take a few hours and immerse yourself in the concept of a world created within a world.

But within the script of this nearly flawless film, there is one term that has raised eyebrows for nearly two decades. Rather than watch the whole film to find it, I’ve put the moment in question here:

(It starts at 48 seconds…)

If you didn’t catch it, they are eating something called “Single Cell Protein.” While this may sound rather futuristic, it comes from a concept developed in the past….

(In the 1960s…)

The idea was to somehow find a way to make food from bacteria. Back then, the concept was considered futuristic and not possible at the time.

But now the future has become reality thanks to a Finnish company called VTT. They have created the first viable single cell protein mixture. You can read more about the story by clicking on the title, “A Team of Scientists Just Made Food From Electricity — and it Could be the Solution to World Hunger

What makes this discovery so interesting is the actual look of the food source…

(Looks like the stuff in the movie..)

The link between VTT and film goes beyond visual appearance. This single cell protein mix is made using equipment that play a major role in the film…


Of course, this cinematic version is quite different from the one used by VTT. First off, the scale is significantly smaller. Then there are the living organisms contained in the reactor. I won’t give away what is inside those fictional reactors but VTT is happy to share what is inside their system…

(“Knallgas” Bacteria…)

The name may seem strange but the decision to go with these types of bacteria is quite sound. Here’s why…

If you happen to speak German, you’ll know that “Knallgas” means “Bang Gas.”

If you happen to know anything about gases, you’ll realize that bang gas is another name for hydrogen.

If you have studied hydrogen utilizing bacteria, you’ll know they use carbon dioxide as an energy source to grow.

Finally, if you have any appreciation for what bacteria produce as they grow, you’ll come to realize that this reactor will end up in the production of single cells filled with proteins and other components such as sugars and fats.

We tend to call these bacteria chemolithoautotrophs but thanks to VTT you can also call them by a different moniker…

(The solution to global hunger…)

As mentioned in the film, single cell protein has everything the body needs. But that isn’t the reason why this discovery could revolutionize food security. That lies in the necessities to produce this nutritious product:  carbon dioxide, water, bacteria, and a source of electricity.

In light of the problems we face with climate change, reduced agricultural space, and an ever-growing human population, this route may be the key to improving health across the globe.

With a little more time and some upscale efforts, we may use single cell protein as a viable means to keep the world’s population fed. Perhaps more importantly, having well-fed people may help to foster brilliant minds from all over the world. This then can lead to even more fantastic and amazing revolutions…

(Unlike this one, which was a true disappointment…)

From Germ Guy to YEGhead…

Normally, I am contacted by the media about three to five times per week for interviews although that number can reach into the dozens over a seven-day period. As a result of the sheer number of appearances, I tend not to post the reports lest this blog be little more than a link hub.

However, I want to share one particular interview from yesterday with you.

(The Ryan Jespersen Show)

If you have about twenty minutes, you can listen to the entire discussion as the topics encapsulate most of the stories I’ve been discussing over the last seven days.

Even if you don’t have that amount of time, I would suggest you listen to the first two minutes as I make an announcement live on air. As to the nature of that announcement, if you are familiar with airport codes, you might already know the details from the title of this post.

If not, this might offer some assistance…

(If, of course, you are familiar with hockey…)

If that isn’t helping, this visual clue may help…

(If, of course, you are familiar with shopping malls…)

If it’s still not clicking, perhaps this can make everything perfectly clear…

(a.k.a. YEG)

Come January 2018, I’ll be leaving the metropolis of Toronto and heading out west to the exquisite environs of Edmonton.

The move is not random, I assure you. This has been in discussion for almost a year and only recently became official. I won’t share the details here but if you wish to learn more, you know how to contact me.

What I can tell you is this. The move has the potential to open up new avenues in the realm of science communication. Being The Germ Guy has brought me to this incredible point in my life. Yet, I have expanded my horizons over the last decade. I hope to increase the scope of my work over the coming years although perhaps not with the moniker, The YEGhead. But who knows…

The process most likely will be slow but I promise you, I will do my best not to lose my mercurial nature. It is a part of who I am and I cannot imagine losing it. Besides, I find it always helps to deal with stories such as one I recently discussed on TV dealing with…

(Germy birthday cakes…)

I hope you will continue to stick with me as I make this transition. I have been thankful for your support over the years and will do my best to keep you engaged and entertained regardless of what place I call home.


Would You Accept A Hepatitis-C-Infected Liver Transplant?

A few days ago, I came across a news article that intrigued me. It involved the practice of performing liver transplants using donors who are infected with Hepatitis C virus. You can read the article here: Could hep-C-infected livers solve New York’s organ-donor shortage?

Right off the bat, you might think this concept would be described best as…

(Who would do such a thing?)

Up until a few years ago, you would be right. The mere idea of transplanting organs, blood, or other tissues infected with hepatitis C was considered completely unethical. After all, you would be giving a person a potentially lethal disease.

Yet, times have changed. Today, there is a treatment for this viral disease with up to 99% success rate. It’s known as…

(aka “The Cure”)

This drug is a combination of two effective means to prevent Hepatitis C from reproducing in the body. One, known as sofosbuvir prevents the virus from multiplying inside the cell. The other, velpatasvir, blocks the ability to assemble new viruses.

With this in mind, the concept of transplanting an infected liver becomes a little less worrisome. After all, if there’s a cure, then why not give someone a shot at living a longer life? It fulfills the human belief that…

(No one would argue with this…)

But unfortunately, there is a catch. The drug is expensive. We’re talking in the region of US$75,000 per treatment. That’s an incredible amount, particularly those without proper insurance.

Upon hearing this number, the usual approach to pharmaceuticals may come into play, which usually sounds a bit like this…

 (Remember, this is a family-friendly blog…)

But the exorbitant cost shouldn’t cause much surprise. Advanced pharmaceuticals such as this drug combination are going to be expensive. We’re not dealing with run of the mill tetracycline, which can be made for pennies a pill. The process of making these drugs is difficult and maintaining proper quality control requires far more effort. Also, Epclusa is not as pricey as other treatments offered, which can be tens of thousands of dollars higher. So, according to its manufacturer, this drug is a bit of a deal in comparison.

I understand this may seem like a defense of the pharmaceutical industry and that for the sake of public opinion you might suggest…

(Which is usually good advice…)

But when dealing with a serious topic such as transplantation, in which the end result is either life or death, the issue of what is the right cost for a drug becomes secondary to the situation at hand.

I do think the amount is too high. Yet this is the reality as we face it. It’s not what most people – other than perhaps stockholders of the company – would like to hear but as we’ve learned in many health-related issues, we have to…

(It never gets easy…)

Which brings me back to the article. Should we use infected livers for donation? I feel if a system in is place that allows the recipient to receive cost-effective and/or fully covered treatment, it may help to lower the burden of waiting lists.

But what if a person is going to undergo the treatment and then be left to deal with figuring out how to deal with the disease? The individual may be faced with a question of prolonged life in a state of continual debt.

At this point, the decision should be left up to the person to decide which is the better option. Then, when the choice is made, we should all stand with that person and say only…

(Also, “I support you.”)


Is Social Media Making You Depressed?

Based on all the hype over social media, most people may think logging on is the equivalent of saying…

(A world of opportunities…)

But last month, a study came out that suggests hopping on to the information highway may have a very different result. Instead of finding joy, the researchers suggest we may be making ourselves…

(You get the emoticon idea…)

The paper is entitled, The happiness paradox: your friends are happier than you and it appears in the journal, European Physical Journal Data Science. While the article is a great read, the overall outcome of this report reveals social media – or at least Twitter – is not a reflection of a democratic society. Rather, it is more like another environment all of us have encountered at one time or another…

(High School…)

Anyone who has walked these halls knows amid the goals of education, life learning, and of course, doing well on exams, there is another mission for many a student. We can call it striving interpersonal relationship success, seeking widespread esteem, or developing a cult of personality. But most people tend to call it…

(A Popularity Contest…)

Much like high school, if you are not popular on social media, then you may be ‘missing out’ on the events and activities others may be experiencing. You may also find a lack of interaction leads to a reduction in self-esteem and self-worth. If things get really bad, you may sink into a quasi-depressive state.

But this isn’t the worst of the situation. In high school, the interaction within the population lasts only about six hours a day and is interrupted by classes. On social media, this effect can be continuous. By seeing the experiences of other individuals and comparing them to yours, you may be amplifying the effect and worsening the potential for…

(Mental Health Concerns…)

From a social perspective, this paper probably makes quite a bit of sense. But mechanistically speaking, there is little information to help us understand why this effect happens.

Thankfully, the answer was found some seven years ago in a paper entitled, A Wandering Mind Is an Unhappy Mind, which was published in the journal, Science.

The study was simple in that the researchers contacted 2250 adults at random times and asked them a series of questions beginning with their state of happiness. With that in place, they asked about what the individual was doing at that moment, whether the mind was wandering, and if so, on what imagery.

When the results came back, the team discovered a wandering mind was in a way similar to what is commonly associated with idle hands…

 (They do the devil’s work…)

Almost half the people contacted were suffering from a wandering mind. When they were asked about the nature of the wandering, most were thinking of pleasant topics while only about a quarter were thinking of unpleasant situations. As one might expect, the latter group were not feeling altogether happy. But even those who were thinking of pleasing situations were also not any happier.

I admit, after I read this, I was probably thinking the same thing as you…

(It makes no sense…)

But when you think about it, those who were wandering to pleasant thoughts were trying to get away from an unpleasant reality. They were not happy to begin with and no amount of daydreaming would help.

As for those thinking unpleasant thoughts, it seemed to be a consequence of a lack of focused action. They were either bored or doing something that required little focus, such as watching television, doing errands, commuting, or trying to keep themselves busy by…

(I’m sure you guessed this already…)

This develops a vicious cycle in which a combination of a lack of focus and low popularity on social media lead a person down a rather unfortunate path of even more unpleasant thoughts.

The best way to avoid all this trouble is to give yourself the opportunity to get away from the contests and the lack of focus. This could come in the form of a good book, a compelling movie or television series, a hobby, skill, or exercise.

There’s also one other activity some may considering. It was found by the researchers in the second study to cause the least amount of mind wandering…

 (If you don’t get this, Google, “The Newlywed Game”)



Consider The Conceit Behind The Concept…

When I wrote The Germ Files I had one goal in mind. I wanted readers to better understand the role of microbes in their lives and in their health. In doing so, I avoided using the names of specific species unless it was warranted. Instead, I grouped the hundreds to thousands of species found in and on our bodies into three major groups.

  • Friends
  • Foes
  • Bystanders

As I’ve learned, this strategy was quite effective as it kept the focus on the information, mechanisms, and any relevant advice I shared.

I also made it very clear this book was composed for all audiences, not just those in the scientific community. This was not a 300 page academic paper. Although the statements were based on over a thousand scientific articles – and some of my own research – I had no intention of regurgitating the information. Doing so would have put me into a corner and limited the reach of my message.

If you haven’t read the book yet, I invite you to pick it up and give it a read because it will help to understand what I am about to discuss.

Last week, a paper came out in the journal PLoS ONE entitled: Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing. As you might expect, this initially caught my eye as it appeared to parallel what I like to call the “good germs friendly diet” I discuss in my book. I was anxious to give it a read.

The concept appeared to be relatively straightforward. A group of 21 volunteers underwent a month-long diet called The Gut Makeover. The paper outlined the diet, which involved the following steps:

  • Three main meals each day with no snacks between;
  • Nothing between dinner and breakfast;
  • Five cups of vegetables and two cups of fruit;
  • Add some protein;
  • Keep the plants varied between 20 and 30 over the course of a week;
  • At least 20 chews per bite
  • Use virgin olive oil and coconut oil as the base for any cooking

As for the restrictions, there were quite a few including refined sugars, grains, alcohol, caffeine, and dairy products.

At this point, the diet seemed to be similar to almost all diets out there. Nothing seemed to be unique.

The difference involved the inclusion of fermented and prebiotic foods after the second week. This included kefir, sauerkraut, tempeh, and miso on the fermented side and a variety of fibre-filled vegetables and fruit as prebiotics.

Once I had arrived at this, I had mixed feelings. All of these recommendations are part of a “good germs friendly diet.” Most also can be found in the best diet for our microbes, the Mediterranean diet. But as this was a “microbiome restoration” plan, I figured there would be some good news to come.

I was wrong.

As the title implies, many of the people who undertook the diet did lose weight and had improved physical and emotional well-being. That wasn’t so bad. What truly disappointed me was the lack of any experiments examining the nature of the microbial population in the gut. Considering the title of the document I figured there might be at least some evidence to show restoration had occurred. Yet there was nothing.

This paper clearly demonstrates the problem with what I like to call conceit.

The article was presented in a manner to convince readers the diet would improve one’s microbial population. One month of dieting would restore the number of friends and bystanders while reducing the number of foes. Yet, there was no experimental evidence to prove this transition occurred.

Which brings me to the most important question this paper didn’t answer:  Did the diet really restore the microbial balance? If you have read The Germ Files, you’ll realize the answer is no. Based on several experiments examining the components of this diet, these are the most likely mechanisms.

  • The caloric restrictions would have led to a reduction in proteins known to form fat;
  • The use of fibre would have led to an increase in intestinal bile and decreased cholesterol;
  • The lack of sugars would have led to increased fat oxidation and adipose tissue loss;
  • The polyunsaturated fats would reduce inflammation;
  • The polyphenols in vegetables and fruit would have helped to balance immune function;
  • The addition of fermented foods would have a short term beneficial impact on health.

As for the microbes? Most of these dietary components are anti-foe and pro-friends/bystanders. So one might expect a microbial shift during the change in eating habits. But unless an individual continues this regimen nonstop, the alteration is temporary. Within as little as three days, the foes would most likely return.

Being able to identify the conceit behind the concept is important because it will help gain a grasp on the real message instead of the one being presented.

This paper is only one example – although probably one of the most obvious I’ve seen in a while – of many we see both in the academic literature and on store shelves. Figuring out which are valid and which are not worth the effort can be difficult.

What I can tell you is that when I write, I concentrate on clarity, not conceit.

I want readers to understand the information in a way that makes sense with as little questions as possible. Those of you who have read my books will appreciate what I am saying. If you haven’t had the chance, I hope you give it a shot.

Finally, I usually don’t market my works as I let them stand for themselves and let the clicks and sales happen naturally. But when I see an article such as this diet paper appear in the literature and subsequently gain public attention, I feel the need to offer an alternative. If my words help to keep people from doubting the influence of microbes in our lives and the microbiologists who study them, I believe it’s well worth taking the risk of being called a conceited self-promoter.








Putting the Poo in Swimming Pools…

Over the last few years, as summer approaches, I tend to receive requests to talk about a phenomenon that might make even the nastiest person go…

(Sorry, Dr. Evil…)

I’m talking, of course, about fecal matter in swimming pools.

I’m sure you may have heard about this occurrence in the news. You may have ignored the story thinking it is another attempt to keep us in the matrix of germophobia. But in this case, the threat is real. Or, to put it another way…

(Thanks, Morpheus)

Feces in pools happens and based on some pretty convincing evidence, it’s more common than you might think. If you don’t believe me, may I suggest you read this wonderful article on the likelihood of finding fecal bacteria and viruses in your local swimming environment.

Assessment of Enteric Pathogen Shedding by Bathers during
Recreational Activity and its Impact on Water Quality

A Microbial Version of Fight Club…

These days, when a scientific article comes out, the title is designed to provide as much information as possible into the specific subject of the study. For those immersed in that branch of science, the words make sense. But for the rest of the population, these titles invoke a rather understandable response…


You can’t blame the researchers. They simply are following the rules of what many call the scientific club. Researchers talk in a certain way and title their papers in a scientifically conventional manner. If you don’t follow, you don’t belong.

Unfortunately, when it comes to that wider audience, researchers understand the mere sight of a complex title can leave many thinking…

(I have made a critical mistake…)

But every now and then, someone chooses to fight this convention and come out with a title that is both wonderfully composed and easy to understand. One such article came out recently in the journal PLoS Pathogens.

The article is split into three parts. The first discusses the function of what is known as a Type VI Secretion System, or T6SS for short. It’s a group of proteins assembled together in the form of well…

(A crossbow…)

Not surprisingly, the role of T6SS – as the name implies – is to send out, or secrete, factors from inside the cell to the surrounding area. As to what these factors do, the deliver what can be best described as…

(A vicious punch…)

When a bacterium feels threatened, it uses T6SS to attack other bacterial cells in the hopes of wounding or killing the invader. The authors even provided a lovely visual description of how T6SS is used…

(I couldn’t have drawn it better myself…)

In essence, T6SS is a survival mechanism designed to help ensure bacteria maintain their territory in a diverse environment.

Which brings us to the second part of the paper, where this battle is happening…

 (The gut…)

There are potentially hundreds of different species living in our gastrointestinal tract, especially in the colon. While we might like to think they are all getting along, researchers have shown this is not the case. Instead, there are microcosms in which bacteria are…

(Facing off…)

Many of the bacteria in possession of T6SS are pathogens capable of causing diarrhea and other illnesses such as cholera. The researchers suggest the presence of T6SS gives them an advantage in our guts and can increase the likelihood of symptoms.

Now it’s time for the third part, which the authors magnificently described in the following image…

(Can you guess what is happening here?)

Let’s make this even easier to understand…

  1. The yellow bacterium is a pathogen with a T6SS in place.
  2. The blue bacterium is a friendly species, also known as a commensal.
  3. using genetic engineering, commensals can be given the ability to produce antidotes to T6SS toxins such that they can defend against attack.
  4. Using engineering to give commensals the ability to make T6SS, they also can engage in battle.

The group suggests using these genetically engineered commensal species may be useful in helping to prevent and possibly treat gastrointestinal infections. While this still is little more than a theory, considering the widespread nature of gastrointestinal bacterial infections, and the rise in antibiotic resistance, this strategy may be well worth…

(Further discussion…)

If you’ve been following along, you probably have noticed I haven’t actually given the title of the paper. I first wanted to go through the article and see if you could guess what it would be called.

Based on the science, you might think the article would be called…

“Prospective genetic engineering of commensal bacterial species
as a novel means to prevent T6SS-mediated bacterial gastroenteritis” 

But no.  Instead, the title is one of the best I have seen in a long time. It is simply and brilliantly called…

T6SS: The bacterial “fight club” in the host gut.

When it comes to scientific papers, titles are simply a collection of words designed to match a particular format. Although they may appear challenging and possibly lead you to forego reading on, just remember, the authors probably had no choice. It’s just part of the scientific club.

But, if scientists had the ability to be a little more like the authors of this paper, I can assure you they would. Because while you may think researchers are highly focused, straight-laced, thinking machines devoted to the club of science – and they are – deep inside many of them, there also lies an inner…

(Tyler Durden…)

I would suggest it’s worth going past the title and learning more about what makes these people work and well, fight, as hard as they do.

Expanding Horizons Into A Brain New World…

To say the last few months have been busy would be an understatement. April and May were filled with events including keynotes, workshops and my usual “Germ Guy” performances. By the time I arrived home, there was only one thing I wanted to do…

(After I take my probiotics of course…)

But amid the chaos, I also took on a new task, which may seem a little odd at first. I decided it was time to start looking at how to communicate a very different type of science. Microbes and the immune system are fantastic but I wanted to delve into another facet of human existence…


This wasn’t a flight of fancy, mind you. It’s been on my mind for quite some time.

It all started a few years back when I was starting to write The Germ Files. I had been hoping to find a way to merge the worlds of microbiology and the brain. My goal at the time was to call the microbial population in all of us, “The Third Brain.” Unfortunately, when it came to making this concept – or if you wish to be accurate, conceit – work, one word came to mind…

(It simply did not work…)

Clearly, I needed to learn more before I could speak about the topic. The only issue with that, however, was a lack of time. I couldn’t afford to put in the effort needed to achieve the right level of understanding. I needed the time to read, read and read some more to gain an appreciation of neuroscience. Then I had to practice writing to effectively communicate.

I’ve been involved in this for about a year but the last few months have afforded me the chance to get comfortable with the topic. I’ve gained the right appreciation needed to go deep into the science and resurface with meaningful and enriching information for the public.

But now comes the hard part…

(Making it entertaining…)

As I continue on this journey, I may interrupt my regularly schedule germy posts with articles and other tidbits from the neuroscience world. If all goes well, you’ll have the same enjoyment factor as those dealing with microbes.

Of course, if I don’t meet your level of expectation, I hope you will let me know…

(Kindly if possible…)

In the meantime, I’ll be getting back to regular posting here on those microbiological and immunological papers and topics I find fascinating. I know it’s been quiet but hope you have not been too offended by the absence.

Oh, if you are looking to see how I have been translating neuroscience for the public, you can check out a compilation of articles I wrote over the last while here: CAN News. I’m sure you will find some of the stories fascinating at the scientific level and I hope personally engaging.





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