The Germ Guy: Confessions of a Mercurial Microbiologist

The Trouble With Cause By Association…

If you happen to keep up with the media, you’ll no doubt encounter health stories focusing on behaviour and disease. Usually, the reports go along these lines…

“A new study has revealed that doing/not doing X can lead to a higher/lower risk for Y.”

The whole point is to make you, as the audience take a step back and think…


These studies are useful as they can help us determine whether certain actions can lead to subsequent health events. They can also help guide policy.

But, there is a rather unfortunate catch. Sometimes, the recommendations arising from these reports contradict each other. The epitome of this conundrum happens to centre around a drink we all know and many of us love…

coffee(A Cup o’ Joe…)

Over the last few years, we’ve been inundated with reports on the health benefits and risks associated with coffee consumption.

On the good side, two to four cups a day may reduce the risk of Parkinson’s disease, ovarian cancer, liver cancer, colon cancer and depression. If you’re a caffeine fiend (like me), six cups a day could reduce the chances for skin cancer.

Reading this list may make you want to say…

garfield(Never mess with an upset Garfield…)

But before you start purchasing those boxes of beans, there is a flip side. Other studies have revealed distinctly different outcomes. Some suggest more than four cups a day may decrease bone density and increase cholesterol. Then there are studies suggesting this much coffee may increase the risk of death by fifty-six percent.

Looking at these numbers might make change your answer to any java offering to…

lemur(I would rather not die…)

From a policy perspective, this information is useful in developing certain recommendations. You can drink two to four cups a day but don’t go any higher. Makes sense, right?

Yet the public perspective is more inclined to be based on an all or nothing principle.  The compilation of these reports can muddy the waters and lead you to drift from Hmm to…


As to why this type of study divergence happens, there is a simple answer. All these studies are observational. The researchers are only looking at links between certain activities in a population of people and what happens to their health over time. This means the results, no matter how robust, only show association, not cause.

We tend to use a specific saying to stress this point:


While this term is extremely useful in scientific realms, in the public forum, it may be considered yet another example of academic elitism.

To get a real grasp of the importance of this cautionary advice, a more appreciable example would provide a stronger perspective. I originally had thought about going through the coffee craziness, but a recent happening may be far more valuable.

This past weekend, I went to a concert for one of my favorite bands…

(Red Hot Chili Peppers…)

I’ve been a fan of their funky music for decades and have loved almost every album. Not to mention, they are perhaps the only group that regularly uses microbes in their lyrics.

Before the concert, I had reached out to the band on Twitter expressing my deep desire to hear a particular song, “Higher Ground.” Many of you might know it from the original singer…

wonder(Stevie Wonder…)

When the concert began however, the set list appeared to follow a path down which this song would not be included. While I was happy to be at the concert, I was feeling a little disappointed.

Then, about two-thirds into the 90 minute show, something magical happened. An incredible bass riff sounded through the concert hall. If you are not aware of it, just listen to the first few seconds…

(The whole song is worth a listen…)

I arose from my seat and starting singing – well screaming – along with the band. This was a singular moment of joy. But I also had another thought that made this experience even more special…

ididit(I caused the song to be played!)

I mean, I did send them a social media request and they did change their song list to suit me. I had to be the cause…right?!

Well, much to my chagrin, the answer is most likely…

goahead(and say NO…)

As hard as it is for me to accept, my one tweet most likely did not lead to a change in the set list. Sure, it might have happened but there was no evidence or mechanism to suggest I was the cause.

Now, if the member of the band I tweeted sent me a response, then there would be a mechanism in place…

  1. I tweeted.
  2. He saw it.
  3. He changed policy.
  4. I benefited.

But without proof, all I can do is surmise and apply conjecture similar to a…

fishing(You get the idea…)

Although the difference between my story and making recommendations for improved public health is an obvious stretch, I hope this at least provides some perspective on the limited power of observational studies. They are useful but need to be examined as a part of a larger picture. Changing one’s actions based on an individual report may lead to trouble.

I hope this example also will engage you to ask a very simple and yet incredibly important question the next time you see/hear/read one of these studies associating behaviour with health…

mechanism(Is there a mechanism?)

If the answer is no, then maybe it’s best to ignore the recommendations until better evidence comes around.


Another Reason Why We Should Never Bet Against Nature…

Over the last decade and a half, one entity has arisen from relative obscurity to being one of the most feared threats. Teams have come together to try and defeat this incredible opponent. Officials have tried to slow down the seemingly indomitable force. Yet, each and every time, failure is the end result and millions are left with what could be described as an itching feeling. It has become clear that when it comes to battle, you simply do not mess with…

(Bill Belichick!)

There is, of course, another threat that emulates the relative craftiness of the head coach of the New England Patriots. This one, however, casts a much wider net across the globe and leaves many more people suffering in its wake. I’m talking about…

mosquito (The Mosquito…)

This small insect has quickly risen to become one of humanity’s greatest public health concerns. Granted, for most of us, the annoyance of a mosquito bite is similar to watching the Pats win yet another Super Bowl…it’s temporary and eventually goes away.

mcnabb(Except maybe in the case of the Eagles…)

Heartbreak aside, for millions around the world, the mosquito situation is far more dire. A single bite can lead to a life-threatening illness. The problem has become so bad that this insect has become recognized as the world’s greatest killer…

deaths(Sorry sharks…)

For years, researchers have been trying to figure out how to stop the mosquito from causing so much trouble. Spraying pesticides has been an old-time favorite but this has proven to be inadequate. Attempts at using natural mosquito killers such as wasps and bacteria may work but they are not widely supported by the general public.

More recently, another approach has shown promise. Instead of focusing on killing the insects, some scientists have attempted to take out critical molecular components needed for reproduction. By genetically modifying these regions, females can be rendered infertile.

In essence, these researchers are trying to take out what I like to call the…

brady(Tom Brady Factor)

The process is rather straightforward. Mutations are incorporated into one generation of mosquitoes such that they simply cannot use the genes. The insects are then allowed to integrate into a community and mate with natural members of the population. The end result is fewer offspring and an overall reduction in the number of these biting pests. Biologically, this is what is known as a…

gene-drive(Gene Drive…)

If you want more information on this technique, you can read more about it here:
‘Gene drive’ mosquitoes engineered to fight malaria.

Early results have seemed promising, yet a major obstacle has been identified. While gene drives may be effective in the short term, researchers are learning they are probably not as useful as once believed. Instead of being a part of a winning strategy, they seem to be ending up being little more than a…

helmet-catch(Helmet catch…)

Granted, this moment was dazzling in display and helped the New York Giants defeat the Patriots. But it was also a fluke that could never be repeated. After all, Belichick returned to raise the trophy not long afterwards.

seattle(Sorry, Seattle…)

As to why gene drives don’t seem to be a long-lasting option, the answer appears to be something scientists always seem to be forgetting when they come up with these ideas. It’s even more unstoppable than Belichick and mosquitoes. We all know it and yet few ever seem to give it the credit it deserves. It’s known as…


It apparently abhors these types of interventions and will do all it can to mitigate them and render them useless. In the case of the mosquito, the introduced mutations are targeted and taken out in a variety of ways. Sometimes, the fully functioning gene is returned. In other cases, natural mutations in the drive can shut it down. Then there is a behavioural component whereby those with the gene drives may interfere with mate selection.

In all of these cases, the end result is the same. The mosquito population thrives and we end up having to once again face…

brady-belichick(A Winning Combination…)

While this discovery may mean gene drives could be going the way of the Rams, Eagles, Panthers, and Seahawks in the fight against mosquitoes, research is always working to find new answers. Sure, the discoveries may not be worthy of your New York Football Giants, but they may eventually offer up a means to keep these insects at bay and help us to improve public health worldwide.

Of course, to accomplish this, researchers will have to be given the resources they need. In addition, they have to be sure to be as sharp and keen eyed as…

(Yeah, yeah, I know it’s hawks…work with me here!)

One more thing…even if you are not watching the game, don’t forget to check out my “Super Bowl Commercials” from a few years back. You can find them here: Super Bowl 2012 Commercials.

A Case of Extreme Vexing…

Every year, an infectious disease spreads like wildfire across North America bringing along with it misery for those who ends up being afflicted. People find themselves rushing to run to the bathroom to relieve that feeling of being sick to their stomachs. Although the condition only lasts a few days, the nightmare is not soon forgotten.

For those wondering, I’m not talking about…

bieber_fever(Although it it quite contagious…)

Instead I’m talking about an illness with many names. Some fifty years ago, it was known as the Winter Vomiting Disease. Then in the 1970s, it was called Norwalk Virus, named after the city in which the virus was originally isolated. Some know it as the cruise ship virus due to its ability to turn a joyful voyage on the sea into a ugly nightmare. Officially, however, it’s known as…

(Norovirus…or noro)

Having studies this organism in the lab, I can tell you it is quite possibly the perfect outbreak pathogen. It has everything going for it…

  1. It can survive for weeks on surfaces – it can be picked up quite easily;
  2. It has a low infectious dose – you only need to ingest a few to develop illness;
  3. It continues to spread after you feel better;
  4. It can resist regular disinfection procedures.

To say the least, this is a true…

eenie-meenie(Eenie Meenie…)

The moment noro finds its way into a confined environment, such as a cruise ship, college dormitory, school, or hospital ward, the situation becomes one of extreme vexing. The virus simply moves its way around from person to person until the entire population has been affected.

To gain any kind of control over this problem, officials need to use equally extreme interventions, such as closing a ward, cancelling the cruise ship trip, or banishing dorm residents for a week. If this were to happen under any other circumstance, it would lead to a massive request for these authorities to say…

sorry(And here’s some money too…)

But when the cause of the conflict is noro, there really is no other recourse.

Although noro hits each year around this time, some seasons end up being far more troublesome than others. The virus seems to affect more people and cause even greater damage. Even more vexing, those who believe they are immune to the virus – because they already had suffered from it – suddenly find themselves back at the toilet again wondering…

mean(What Do You Mean?!)

This happens to be one of those years. It’s not really anyone’s fault, mind you. The trouble is due to the natural ability of the virus to evolve. Much like that other, more famous virus, influenza, noro has several circulating strains, known as genotypes. Just this year alone, the CDC has estimated the number of virus types spreading in the United States is at least six…

norovirus(Although not distributed evenly…)

Unless a person happens to have had come into contact with all of these different genotypes, the risk for infection is always present. This sets up a rather inconvenient truth in which we much admit no matter how many times we may end up with the illness, we must…

neversaynever(No matter how much we would like to…)

There is a small bright side to this situation. Unlike respiratory viruses, noro needs to get into our gastrointestinal tracts in order to harm us. There is only one cell type the virus likes to attack and it’s deep inside the intestines. If we can prevent entry of the invader, we may be able to stay safe.

Granted, this does mean we have to ask one question…

wherenow(Where Are U Now?)

Yet as this image suggests, the answer is relatively easy. Most of the time noro spreads, it’s because it was on someone’s hands. People can pick up the virus from a surface, such as a sink tap or a washroom door handle and readily transfer it to other surfaces or, in the case of self-inoculation, the mouth.

Contamination of objects may not lead to an outbreak. But, when hands come into contact with food, all bets are off. This route usually is the one causing large numbers of infections in restaurants and on cruise ships. Usually, the incident occurs because one or more people simply did not wash their hands properly prior to handling fresh foods not meant for cooking. The end result sadly, is a mass of people disposing of their recent meals from both ends.

This latter situation is exactly why adhering to food safety protocols is so important. It’s also why I feel avoiding even the simplest actions to keep food safe makes…

nosense(No Sense!)

As each year passes and more cases are recorded, I imagine the virus will reach a certain level of infamy. People all over the world may find themselves wanting to avoid the gut-wrenching symptoms and those days of vexation. Granted, it won’t be easy as noro is an able opponent. Yet, as far as I can see, all we need is a combination of purpose, prowess, power and possibly…


With these in place, we can do our best to ensure the virus stays out of our guts for good.

PS: Have you ever had norovirus? If you have, let me know how it felt.

PPS: For the record, I had it and hated it although not as much as when Chris Pronger pretty much did the same thing to the Ottawa Senators during the 2007 Stanley Cup Finals as he did to Bieber yesterday.

A New Type of Vaccination…Against Alternative Facts

This week, the average American experienced a taste of what it is like to be a public health official or researcher. It wasn’t due to an outbreak or epidemic, mind you. It had to do with this…

inauguration(Inauguration Day…)

Despite what your eyes might see above, several people claimed the crowd attending the 2017 event was more populous than that in 2009. A variety of statistics were thrown around to support this view. Even the centre of all that attention entered the debate suggesting he felt there were far more people than the visual evidence suggests.

This all culminated when a spokesperson who was questioned about these obviously inaccurate conclusions suggested they were…

alternative-facts(Alternative Facts…)

As you might expect, this started a rather heated debate in the media and the term itself went viral on social media. Even Merriam-Webster, the dictionary company, entered the discussion pointing out…

fact(To much rejoicing I might add…)

Yet despite all this, those siding with the 2017 claim did not budge.

Right about now, you might find yourself experiencing a tinge of malcontent. Depending on how long this simmers (or festers), you may end up wanting to…


But as much as I hate to say it, for public health officials and researchers, this is par for the course. Each and every day, these wonderful people watch helplessly as evidence is set aside and replaced by a combination of alternative facts, feelings, and conjecture. If they try to set the record straight, they are met with a combination of derision, defamatory comments, and accusations of…

dog-cat(Illiteracy…my favorite)

Using alternative facts to push a claim is a common practice in many different scientific arenas. Three of the most popular – and for the record, false – claims happen to be…

  • Vaccines cause autism.
  • GMOs are going to harm us.
  • Climate Change is not real

No matter what evidence from the scientific literature is presented, those who stand by these claims never let up. Instead, they share a variety of alternative facts in the hopes of confusing the public. What they are doing is relying on one of the fundamental tenets of science:  it is not absolute…

zero(Except, of course for Absolute Zero…)

Because scientists cannot conclude with complete certainty, alternative facts can squeeze into the discussion and eventually overtake it. Depending on the index case – the person who introduced these falsehoods – misinformation can spread like a virus. An outbreak may ensue and if not caught early enough, quickly turn into an epidemic of speculation, doubt, and lack of trust.

This analogy, while depressing, does offer some hope and a possible hypothesis to counter alternative facts. It goes something like this…

Because alternative facts are viruses of fiction,
we can vaccinate against them using factual information.

Okay, I know what you’re thinking…

what(He’s lost it this time…)

I admit, it does seem far-fetched. Yet, a group of researchers based in America and the UK, this theory appeared to be worthy of at least a preliminary test.

The team focused on climate change as the topic of interest. The virus, if you will, is the continuing perception that it does not exist. The vaccine was comprised not of a liquid injected into the arm, but a flood of factual information injected into the brain through communication.

Here’s how the experiment worked. The team conducted an online survey in which hundreds of people were asked about their view on climate change. Then, they were exposed to information regarding the phenomenon. The messages fell into one of the following categories:

  1. A consensus statement on climate change – it is happening;
  2. Alternative facts (which they called a counter-message);
  3. A simple vaccine comprised of easy to understand information about climate change;
  4. A stronger vaccine comprised of detailed knowledge and information on climate change.

After the exposures were complete, the volunteers were asked again for their views.

When the results came back, this is what they saw…


(The numbers here reveal the change in people’s views from their original stance…)

As you can see, the power of alternative facts (Line 3) is undeniable. These untrue perspectives were able to change the viewpoint of close to 10% of the people. They also are effective at in neutralizing an opposing message. Just look at Line 4. Even though the consensus statement was made, as soon as those viral entities made their way into the brain – especially for Republicans – the stance changed for the worse.

When you think about it, this is why people who want to avoid the truth turn to alternative facts. They know these distractions from reality can sway a person to doubt and possibly force them to turn away from what is known to be true.

But the real story comes in the subsequent lines. Line 5 is the simple vaccine while Line 6 is the stronger version. Both were effective at helping to sway the stance towards the evidence. Even when those alternative facts were presented, they had little effect. In essence, the vaccine had worked.

When it was all said and done, the vaccine wasn’t quite as effective as they hoped. The effectiveness was only about 20%. If this were a real biological vaccine, it would have to go back to the drawing board. However, for this purpose, a change of 20% of the population could be regarded as…

yuge(Sorry, I had to…)

When you think about a population of hundreds of millions of people such as America, swaying that many minds towards reality over fiction would be considered a triumph.

Of course, this study was done in a controlled setting using surveys and volunteers. No one quite knows if it would be as effective in the real world. However, for those who continue to spread the good word, this study should provide some comfort. The more these people continue to vaccinate the public, the greater the chance we may all be able to live in a world ruled by scientific evidence instead of…

pinocc(You get the idea…)

If you want to read the entire study, you can find it here: Inoculating the Public against Misinformation about Climate Change – van der Linden – 2017 – Global Challenges – Wiley Online Library


A Tragic Tale From Antibiotic Resistance Country…

It’s amazing how time flies. It seems like just yesterday we could go into a doctor’s office with a bacterial infection, undergo a quick examination, and be sent on our way with an antibiotic prescription. We knew we would get better and get back to our normal routine without any concern.

Back then, medicine was considered a given and no professional was thought to be…

gambler(A Gambler…)

Today is a much different story and medical professionals everywhere are realizing treatment is more a game of chance than an action of certainty.

This change in predicament is all thanks to a natural process used by bacteria to stay alive in the environment. Scientifically, this phenomenon is an evolutionary process in which the genetic makeup of the bacterium changes such that it can produce proteins and other molecules allowing it to tolerate the presence of biologically toxic molecules. But most people simply refer to it as antibiotic resistance.

Since its discovery back in the 1940s, resistance has changed the medical landscape
like a…

ring-fire(Ring of Fire…)

In the last few years, almost everyone has since heard about the rise of resistance and the threat of what is being called the post-antibiotic era. Even the World Health Organization has deemed the current situation a crisis. Still, for most people, keeping this worry at the forefront has been difficult at best. After all, we can still go to the doctor and get a prescription that works.

But reality may have finally hit home and more people may end up thinking about antibiotic resistance as much as I do. It’s…

always(Always On My Mind…)

Last week, the media reported on the tragic death of a women in Nevada. The story, which was published by the CDC, sounded like it came from the pages of a novel. She was in her 70s and had shown up at the hospital with what was assumed to be a mild hip infection. The doctors gave her antibiotics but they didn’t work. They tried again and again but there was simply no change in her condition. Eventually, the bacteria entered her blood – a condition known as sepsis – and she eventually succumbed to the shock.

When the doctors sent the bacteria for testing, their worst fears were realized. The cause of the infection, a species known as Klebsiella pneumoniae, was resistant to all available antibiotics in the United States. There was nothing that could have been done.

If you’re like me, just hearing this story might cause you to…

falltopieces(Fall To Pieces…)

But there is some solace to be had. The woman did not acquire the infection in America. She had been in India and had been to a hospital there for surgery.  The bacterium was not native to the United States and thankfully, a search in other areas of the hospital revealed it had not spread. This was, in essence, an isolated case.

That being said, this story of life and death sends an ominous message. In some parts of the world, antibiotics simply cannot save the day. A visit to the hospital may no longer be considered a means to resolve a health condition. Instead, much like before the advent of antibiotics, the house of health may once again become a…

heartbreak(Heartbreak Hotel…)

Hope is not lost, however. Although antibiotic resistance continues without any sign of slowing, researchers are doing their best to find ways to combat the resistance.

This is, however, no easy task as bacteria have a significant advantage over us. They quickly evolve and can share resistance mechanisms with one another. For any scientist, taking on this task is daunting. Trying to find answers is even more challenging. Commitment is a necessity and one must accept this job requires more than just…

ninetofive(9 to 5)

Thankfully, the work is leading to victories. For example, researchers recently have revealed a way to ‘reverse’ a certain type of antibiotic resistance. They have developed a molecule capable of stopping the mechanism used by certain bacteria to resist several antibiotics. It’s not quite a watershed moment but it is comforting to know progress is being made. You can read about this discovery here: Molecule shows ability to thwart pathogens’ genetic resistance to antibiotic.

For the most part, the war on resistance is being fought in laboratories and healthcare facilities meaning there is little we can do to join the battle. Yet, there are ways we can help keep the scales tipped in our favour. All that’s needed is to take a closer look at how we ride that horse called life and figure out a new way to get…

saddle(Back In The Saddle Again…)

We can pay closer attention to hygiene. We can comply with proper food handling and cooking processes. We can avoid medical tourism and make sure we are vaccinated when we travel to certain areas for the world. Perhaps the best choice we can make is to avoid meat from animals raised on antibiotics.

If you have added these activities to your daily life – even if it’s not to reduce the spread of resistance – I thank you. They may seem like small actions but they can make a big difference when done en masse.

Granted, it will take time before we see an anti-resistance movement. Yet this woman’s tragic story may convince more people of the dire consequences we face. To be honest, this can’t happen soon enough. We need people to identify with the problem, appreciate the risks, and realize what needs to be done now.

In essence, for us to win this war, we need everyone to say…

light(I Saw The Light…)


A Moment That Changed The World…

Late last year, something unbelievable happened. As news spread, the world woke up to a new reality. Nothing would ever be the same again.

Most people were shocked by the revelation, as it was thought to be impossible. Yet a handful of people knew this would occur. Almost no one believed in them but they continued on tirelessly. They did everything they could to skew the odds in their favour. They hacked what was once thought to be an impenetrable defense and used viral tools to ensure success. In the end, their efforts paid off and these once slighted individuals reaped the rewards with almost sinful delight.

If you haven’t already guessed what that event was, I’ll fill you in…

(The Ebola Vaccine was 100% Effective!)

Believe it or not, vaccination proved to be perfect in the most recent clinical trial. For researchers, public health officials, and even the World Health Organization, this was a hallmark moment. It was time for a…


If you hadn’t heard of this incredible news, you can’t be blamed.  The article came out right before Christmas. Most people including the media were rightfully focused on the festive season of the Holidays. They also were dealing with the hangover of another world-changing event that happened six weeks earlier…

trump-pres(Which, if you didn’t know, culminates today…)

If you think about it, there were similarities between these two events. The premise of a President Trump or a 100% effective vaccine was considered ludicrous just a year before. Although both had shown themselves to be capable of achieving these heights, few really believed they would succeed. Yet, as the human tallies came in, the picture became clear. At the end of it all, there was only one word to describe what had occurred…


But there is one significant difference between these two announcements. One has created a significant amount of debate, backlash, and concern while the other has created a sense of hope not seen since…

hope(Susan Lucci’s Winless Streak Ended…)

Putting the parallels with American politics and daytime soap operas aside, there are three reasons behind the optimism from the Ebola vaccine. The first and most obvious is a future in which epidemics like the one seen in 2014-2016 may never happen again. After everything the people in the West African nations of Guinea, Sierra Leone, and Liberia went through (and yes, America), this announcement provides…

relief(Some welcome relief…)

The second has to do with the ability of a vaccine to protect. For what might be the first time, there is an option with 100% effectiveness. This has always been the goal of researchers but until recently, figuring out how to develop the perfect candidate has been nearly impossible. A new benchmark has been set against which future vaccines will be evaluated. Granted, finding a way to protect against Ebola is much easier than say…

flu(A constantly evolving virus…)

Yet even flu researchers are getting closer to a universal vaccine that may one day protect us against all possible variations of this more common – and possibly more troublesome – pathogen.

The final reason deals with the nature of the vaccine. It was made through a combination of different genetic engineering processes. The virus used isn’t even Ebola but one that is harmless to humans. Although it is officially known as a recombinant, some might prefer to call it a…

gmo(Genetically Modified Organism…)

As you probably know, there is a significant amount of debate on GMOs with good reason. These products have entered the agricultural industry and the food marketplace without much consultation or information being given to the public. Not surprisingly, some have reacted quite negatively to this and called for an all out ban on genetic engineering.

But thanks to this vaccine, we can realize not all genetically modified organisms are bad. After all, if you want to look at a GMO, all you need to do is…

timberlake(You are not a clone…)

Perhaps this good news GMO story may balance the scales a little. Maybe those calling for an end to this technique will realize it only can hurt scientific advancement and put other discoveries such as this vaccine in peril.

I hope all people will understand the need for genetic engineering in health and medicine and appreciate the potential it brings. Most importantly, I wish all those who are skeptical of scientific research understand for the most part, the work, while at times seemingly out of touch with reality, ultimately is attempting to improve our world and make it a better place for all.

Okay, I know that may have sounded like an…

inaurgural(Inaugural speech…)

But as this day only comes once every four years, I figured it would be worth the risk.

If you want to read more on the vaccine, you can check out the World Health Organization for more details:  Final trial results confirm Ebola vaccine provides high protection against disease.

A Bacterial Bakery Trick…

It’s a common practice for bakers. They arrive early in the morning, spend hours slaving in the back, and eventually get all the freshly made breads, cakes, pastries and buns organized in displays. Then, when the time is right, they invite the world to enjoy the wares of their labour by…

bakery(Opening The Door…)

If you happen to be walking by at just the right time, the attraction can be almost irresistible. The aroma coming from the freshly baked goods can stop you in your tracks and lead to an unexpected diversion into the store.

Scientifically speaking, this attraction is caused by a phenomenon known as odorant perception. An aromatic molecule called a volatile organic compound enters the nose or the mouth and interacts with the cells resting inside. As this happens, olfactory nerves sense the molecule and send a signal…

aroma(To the brain…)

Here’s where it gets interesting. The scent first is interpreted as either pleasant or repulsive. After the decision is made, a neurological signal is transmitted to the rest of the body to move. Pleasant aromas tell our bodies to get closer to the smell while those considered to be foul force us to move away.

If we rely on instinct alone, our bodies heed the command and we head, if only slightly, in the appropriate direction. If the smell is strong enough, it may even overcome our current mental plans. This is most common in repulsion, when being overtaken by a horrific odour causes us to move away quickly.

But, those clever bakers use the opposite reaction to their advantage. If they can make those wonderful aromas as strong as possible, people will fall victim to instinct and…

bakery2(Pick Up A Few Things…)

Odorant perception isn’t only for humans. Researchers have found other species rely on this phenomenon. Mice have it, fruit flies have, even worms have it. The response to external odours appears to be conserved in evolution…at least in animals. Until recently, no one quite knew if the use of volatile scents could attract or repel bacteria.

A few weeks ago, that changed when a team of researchers from McMaster University discovered a bacterial species capable of using odours to signal other members of the same species. It’s known as Streptomyces and it is the source for many antibiotics – think streptomycin. But the bacterium also has a rather fascinating capability. It can change the way it looks and functions over time…

streptomyces(Here’s the life cycle…)

The bacterium also likes to explore its environment in search of nutrients. However, this is no easy task. Those cells designated with the burden of exploring may encounter a long and arduous trip. They may have to travel great distances (millimetres) from the colony. They may face unspeakable challenges including giant chasms (agar cracks), rushing rivers (condensation), and of course, great mountains…

rock2(…or as we call them, small stones)

Depending on where the new resources are eventually found, these brave bacteria may be isolated in a brand new world without any means to signal the colony.

But thanks to this paper, there really is no reason to fret. We now know Streptomyces can use the same method as bakers to let their colleagues know food has been found and that more cells should come.

Here’s how it works. Upon finding the nutrients, the bacteria create a volatile organic compound – an aroma – that can travel through the air back to the colony. This airborne chemical reaches home base and informs the other members about the new source of food. Other explorers are then sent off like pilgrims to join these brave scouts and ensure the population continues to thrive in this new, rural area of the world.

At the end of the day, the explorers are joined by their peers, the colony extends and much like those who found new food at the bakery…

rock3(Everybody wins!)

There is, however, one particular difference between the lure of the baker and the signal from the explorer cells. That happens to be the nature of the volatile organic compound causing the attraction.

Humans tend to love chemicals such as maltol and methianol, which give off that fresh bread aroma. We simply cannot resist. But the bacteria have no interest in these molecules. For them, nothing is more delightful than trimethylamine. It’s what drives them to explore and is the key to their movement in this paper. For those who are not familiar with this scent, it’s most commonly associated with…

deadfish(Rotting fish…)

Guess it’s true that there are different strokes for different folks…or in this case, bacteria.

If you want to read more on how Streptomyces uses volatiles to communicate, you can read the entire paper. It can be found here:
Streptomyces exploration is triggered by fungal interactions and volatile signals

Three Germy Cheers For The Appendix!

Sometimes a study comes out and you have no option but to get excited because the topic is simply…


Okay, so maybe the appendix isn’t exactly what you might consider headline news. After all, it’s long been considered an evolutionary artifact with no real use in humans. Yet, in the city of Glendale, Arizona, a research team at Midwestern University have revealed this tiny organ may indeed serve a valuable purpose.

It may be a safe house for friendly bacteria…

skeptical(Yeah, I know it sounds sketchy…)

This theory has been around for about a decade but no one has ever been able to explain it in a credible manner. Thankfully, that’s what the researchers as Midwestern University set out to do in a very systematic and painstaking way.

They took genomic information from 533 different species, all of which had some indication of an appendix. Some of them were definitive while others were more sketchy in nature. Some of the more obvious ones (and one non-existent one in G) can be seen here…

(Can you guess which animals they are?)

With the species in place, the team then went about organizing them in a timeline of evolution in the hopes of finding some reason for this intestinal tag. They did this by comparing a variety of different gastrointestinal structures, such as the cecum area. Scores were made based on the shape, size, and function of each part of anatomy. Then environmental factors were thrown into the mix, such as latitude and longitude, population density, and diet.

By the time it was all said and done, I’m sure they were not in the mood for….

ribbit2(Singing and Dancing…)

But, the results paid off as they were able to develop several links between evolution and the appendix. Most were anatomical in nature but one significant link got me in the mood for some MALT!

malt2(Not that kind…)

The appendix is rich in two forms of immune tissue, gastrointestinal associated lymphatic tissue (GALT), and mucosal associated lymphatic tissue (MALT).

kermit2(Get it?)

Both these immune types are specifically designed to help us deal with whatever comes into the gastrointestinal tract. Having more GALT & MALT can also be good for our friendly bacteria. The cells in this area help to stimulate the growth of several beneficial species through a variety of chemical cross-talk mechanisms.

In essence, having that appendix might help ensure you have a healthy and diverse microbial population that is…

telus-frog(Sitting Pretty…)

Of course, all of these theories are still up for debate. Even this study suggests there are many questions to be answered before we can truly say the appendix is a microbial safe haven. Yet, this study adds to the theory that as we evolved through time, our bodies learned how microbes are for the most part our friends and wanted to be sure we loved them biologically.

Now if only we could love them emotionally like we do….

frog-kiss(You get the idea…)

For more on the paper, which sadly is not open-access but I felt definitely worth discussing, you can read more at ScienceDaily: Appendix may have important function, new research suggests.

Oh, and as for those intestinal drawings, here are the answers:
(A) Wombat (Vombatus ursinus);
(B) Brushtail possum (Trichosurus vulpecula);
(C) Rabbit (Oryctolagus cuniculus);
(D) North American beaver (Castor canadensis);
(E) Rock hyrax (Procavia habessinica);
(F) Orangutan (Pongo pygmaeus);
(G) Bush-tailed phascogale (Phascogale tapoatafa).


The Food Label I Want To See…

I know it’s a week into 2017, but let me first wish everyone a Happy New Year! I hope the turning of the calendar was filled with joy, celebrations, and of course fireworks…

microbe-fireworks(Even if they weren’t microbial…)

Over the last few weeks, I’ve been busy talking in the media on one of the most common topics around this time of year…

resolutions(Did you make a list?)

Two of the top goals are weight loss and getting more exercise. I’m sure that at one time or another you or someone you know has made a promise to achieve these very important objectives.

But even if we strive to shed the pounds and get a little more toned, the odds may be against us. Though we may blame peer pressure, lack of willpower, or some other understandable excuse for not getting the results, there could be another reason for the failure…

gut(Gut microbes…)

Quite a few studies have come out showing both of these goals can only be achieved when you have a highly diverse population of bacteria. When diversity drops, so does the potential to regain health through these resolutions. This condition of having poor microbial diversity has even been given a buzzword and definition…


For ecologists this statement makes sense. After all, we are all individual biospheres made up of trillions of cellular organisms all trying to co-exist. If we can maintain a good diversity, everyone wins. But if certain species tend to win out over others, bad things can happen.

How bad can it get? Well, a good part of a certain book examines these troubles…

germ-files(Did anyone get it for Christmas?)

If you are looking for a more academic perspective, there’s an option for you too…

hmh(Notice the co-editor?)

For people undertaking resolutions, the two most important consequences of dysbiosis happen to be improper weight and energy balance. In terms of diet, dysbiosis can resist an attempt to increase diversity for longer than most detox/cleanses/fads last. As for exercise, fatigue and diarrhea are common side effects of dysbiosis. Unless people persevere through the pressures – both mentally and physically – they are likely to…

garfield_faceplant(You get the idea…)

This isn’t the worst of the story. Thanks to years of studying the effect of diet on microbial diversity, one particular way of eating appears to have the most likely chance of leading to dysbiosis…

unhealthy_fast_food(The Standard American Diet…)

This isn’t new information, of course. For close to half a century, we’ve heard about the health troubles associated with this diet. In essence, everyone knows this diet is bad.

Thankfully, many food companies have heard this message and sought to improve the situation. Unfortunately, their idea of changing the product is a little different than the recommendations from public health experts…

labels(Put a label on it!)

Of course, these fancy labels usually refer to only one particular aspect of the product. They also rarely have any real information on the health benefit. You are asked to trust the manufacturer and blindly buy the product.

I’m not a fan of this type of marketing but I also know this is the current reality. Nothing is going change. So, in that respect, I’m going to take the approach of a particular carrot-munching critter with a distinctive New York accent…

bugs-bunny(If you can’t beat ’em, join ’em)

Instead of asking companies to give up on the myriad of different types of single-benefit labels, I think it’s time to suggest a new kind of addition to the package. But this time, make the claim universal in nature. Make sure it takes into consideration both humans and microbes.

In other words…show us your product…

dysbiosis-anti(Does not contribute to dysbiosis…)

I know this is a long shot and never may be given any consideration by food production companies. But, I have to ask…if you knew a label would help to ensure improved microbial diversity, wouldn’t you like to see it? Perhaps more importantly, if you didn’t see this label and were not sure if it could lead to dysbiosis, would you be more inclined to leave it on the shelf?

Let me know what you think in the comments. I would love to hear your thoughts on diversity, dysbiosis, and diet.

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