The Happy gut

A detailed look at the microbiota and how to manipulate it for optimal health

How We Wrecked Our Guts

Posted in microbiota on October 6th, 2017

There is great deal of evidence to show that our guts used to be in a much healthier state decades ago. For example, the Hadza in Africa, one of the last ‘hunter-gatherer’ species on the planet, appear to have 300% more bacteria in their guts than we do. It seems that over time we have lost many of these bacteria, and whatever functions they once provided.

In terms of gut health, one metric that’s often used is diversity. Similar to the environment, it’s often thought that the health of any ecosystem is related to the number of species in it and their relative abundance. Harmony is basically where you have a lot of species, with a mostly equal membership. If any one species starts to take over and populate excessively, it endangers the entire ecosystem.

This is similar to the gut microbiota. Any overgrowth of a particular species can tend to cause problems for the health of the entire individual. Likewise, certain species seem to be protective against ailments like diabetes and obesity – a person generally doesn’t want to lose them.

The Danger of Antibiotics

When I was a child, my mother would take me to the doctor’s office when I was sick. They would perform a bunch of tests, sometimes putting cotton swabs in my nose or throat, and then wait a few days to see what I was infected with. If it was something treatable, often I would get a prescription for an antibiotic and take it home. The key difference back then was they often wanted to know what the bacterial infection was before prescribing the antibiotic. Nowadays most doctors simply prescribe broad-spectrum antibiotics, which are mostly non-specific with regards to the bacteria they tend to kill.

There’s no question that antibiotics save lives. But nowadays doctors are pretty eager to prescribe them, and patients have been trained to basically ask for them whenever there is an issue. The body has an amazing ability to heal itself and fight off disease, but most of us don’t want to go through that process and instead simply opt to take antibiotics whenever we are ill.

The problem is that antibiotics have a massive detrimental effect on the gut microbiota. In one study I read, one course of antibiotics caused persistent changes in the gut for over two years. Some species can be totally eliminated by antibiotics, and never return. Over time this has led to a gradually declining gut microbiota in North America, one that’s getting further and further from our Hadza counterparts in Africa.

I would never tell someone not to take antibiotics, but for myself I actively avoid them whenever I can. The last time I had any antibiotics was a few years ago when I had a surgery, and my gut health has never looked better. If I got really sick, I wouldn’t hesitate to take antibiotics. But for the average cold or periodic infection, I personally steer clear of them myself.


Another aspect of gut health that is causing damage is the preferential shift to c-section deliveries in many countries. There are two problems with this.

First, there’s growing evidence that a child acquires its initial microbiota from its mother during delivery through the birth canal. C-section babies, since they don’t pass through the birth canal, instead end up with a microbiota that resembles the bacteria on the walls and equipment in the hospital, one that looks nothing like what a typical healthy microbiota is supposed to represent.

The second issue is that during a c-section antibiotics are usually administered, which has the effect of further damaging the microbiota of the mother and baby, depending on the timing of the antibiotics.

While there are many medically justified reasons to have a c-section childbirth over a natural birth, the trend in many countries to do it primarily for convenience or cosmetic reasons is increasing.

Breast Feeding

There’s a long line of research that shows that breastfed babies are generally healthier than ones fed formula. This seems to be the case as well in terms of the gut microbiota. In fact, there are certain elements in breast milk that can only be consumed by certain bacteria in the gut – without them they would pass right through the body. So this shows at some level that breast milk has evolved to not only feed the baby, but the baby’s microbiota as well.

Excessive Cleanliness

Another aspect which is hurting our gut microbiota is our excessive cleanliness. There are antibiotics unfortunately in many places now, and most people probably aren’t aware of them. For example, some toothpastes have ingredients in them that effectively act like antibiotics. Those hand sanitizers that many people use also are good at wiping away bacteria on our hands, many of which may be beneficial to the body. The chlorine and chloramine in our water also kills bacteria in the body.

Research has shown that children who grow up on farms have improved health in general, and one theory about why this is rests in the fact that they are exposed to far more germs and bacteria than kids off the farm. This causes the immune system to be far stronger, and seems to show that they can fend off more pathogens and diseases. So our excessive fear of being dirty may be causing our immune systems to be weaker.

Research has shown that in families with dogs, they not only have a healthier microbiota but also the microbiota of family members are more similar to each other. So Fido the dog is not only an important companion, but he’s helping to transfer beneficial bacteria (through licking and being outside) throughout the house.

So in terms of gut health, what does all of this mean? I can’t instruct others on what to do as these are personal decisions, but for me I avoid hand sanitizers (nothing wrong with a little water) and antibiotics whenever I can. I haven’t quite found the perfect solution to removing chlorine/chloramine from water, but I am actively looking for a good solution. But in general, I try to avoid anything that I think will hurt my microbiota.

In the next newsletter (sign-up here!), I’ll talk about some common ways you can improve your gut health, primarily through what you are eating! We’ll discuss fibre (digestible and non-digestible) and the new term, Microbiota Accessible Carbohydrates (MAC).

The Exciting World of the Gut Microbiota

Posted in News on September 20th, 2017

In 2004, the Human Genome Project was completed. The goal of that project was to sequence the entire human genome, ultimately revealing the cause of a majority of ailments in the modern world.

Instead what it revealed was that most of us share over 99% of our genetic code, and that 1% difference doesn’t seem to explain many of our diseases. So if our own genetics aren’t entirely responsible for if we are healthy or sick, what else potentially can be?

The answer to that question came shortly after the development of 16s rRNA sequencing technology – technology which allows us, for the first time, to take a detailed look at the complex bacterial organisms living in our guts and each of their roles. Rather than being benign spectators in our lives, it turns out that these bacteria have developed a symbiotic relationship with us throughout our evolution.

In terms of genetic code, the bacteria in our guts harbour more than 10x the genetic information that’s contained in our own genome. Stated another way, if our genes represent the blueprint to build a one bedroom condo, theirs represent a blueprint to build a ten bedroom mansion. So while our own genome may not explain the various diseases and ailments that are prevalent in the ‘diseases of civilization’ (diabetes, IBS, obesity, chronic fatigue syndrome, etc.), perhaps theirs do?

So far the research is showing that in fact that’s very likely. Each of these diseases appear to have a distinct microbial signature – a collection and pattern of bacteria that essentially acts like a fingerprint identifying a particular disease. Not only that, but manipulation of these bacteria by antibiotics, probiotics, and even fecal transplants (to be discussed in more detail in a later weekly update) often seems to lead to improvement or remission of various diseases such as IBS.

There is a lot of evidence to support this as well. One observation that’s previously been made is that cleanliness does not necessarily contribute to improved health – children who grow up around dirt and farms are typically much healthier. This is known as the ‘hygiene hypothesis’. Up until the discovery of the gut microbiota and its role, there wasn’t really a plausible explanation for why that would be. But antibacterial soap, toothpastes, chlorinated water, and various other ‘clean’ aspects of our society all help contribute to the eradication of various bacteria in our guts.

While research is still in its infancy, this is obviously a very exciting time in health. Various ailments such as obesity and diabetes have often been thought to be progressive and nearly irreversible. But if it turns out that the bacteria in our gut may ultimately be contributing to these diseases, then it may be possible to manipulate them in such a way to reverse or even completely resolve them.

The truth is though we still have a long way to go to figure out what’s going on in our guts. We’ve identified the likely key players, and what they seem to be doing, but we are still mostly in the dark about how to make permanent and consistent changes in the microbiota, at least in terms of improving health outcomes. Taking probiotics (those little capsules you can buy at the store) often seem to help people, but they don’t colonize the gut and so their effects are just temporary. As research continues to progress, hopefully we’ll gain a greater understanding of the contribution the gut microbiota to both health and disease, and better learn how to manipulate it in our favour.

In the next update I’ll talk more about how this all happened – that is how we went from having healthy gut bacteria to our current state, where many people have dysbiotic (unbalanced) or even pathogenic gut profiles. And as you’ll see, the modern world and many of its conveniences are likely the root cause of this drastic change.

This post was original part of The Happy Gut weekly newsletter – if you’d like to receive timely updates about the microbiota and how to keep your gut happy & healthy, sign-up here

Probiotics, Prebiotics, and Synbiotics – What’s The Difference?

Posted in Supplements on February 8th, 2017

A common complaint these days when it comes to gut health is that it’s a difficult landscape to navigate. If ones goes to the health store, they are presented with a pile of different options in terms of prebiotics and probiotics, each with their own idiosyncrasies.

If you occasionally find yourself scratching your head when you walk into a health food store, then this post should help sort you out.


A probiotic is basically a capsule (or sometimes a powder) that contains beneficial bacteria. Once these are ingested, the will hopefully make it past the acid in the stomach and eventually into the gut, where they will contribute their awesomeness. And while it’s true that probiotics can lead to improved health outcomes, one thing to be aware of is that most probiotics do not colonize the gut. They are like people who come to your party – they make it a lot more fun while they are there, but at the end of the night they are probably going home (if you’re lucky).

What that means is once you start taking a probiotic, you usually have to continue taking it to receive ongoing health benefits. If you look at the price tag for a lot of probiotics, that can be a significant investment going forward. So a person really has to weigh the pros of the treatment with the cons of the cost. For many people though, the cost isn’t really a huge burden if they can actually achieve a better health outcome.

Common probiotics these days usually contain some type of bifidobacterium and also some lactobacillus, but there are many different types. You can take a look at a current listing of probiotics on Amazon.


Prebiotics are different beasts entirely. Instead of adding new bacteria to your gut as they pass through, prebiotics are fermentable food meant to feed the beneficial bacteria that are already in your gut. While most healthy food has some type of fermentable carbohydrates in it to help feed your gut, prebiotics are typically refined sources of particular types, such as resistant starch or oligofructose.

Here are some examples of prebiotics on Amazon. I’ve personally used the prebiotin power myself, and it helped to increase bifidobacterium in my gut.


In case you haven’t guessed yet, synbiotics are combinations of both prebiotics and probiotics, meant to give you the health benefits of both. Often they will be combined in such a way that the prebiotics are meant to feed the specific bacteria contained the probiotics, giving a person a double whammy.

So next time you head down to the health food store, you’ll have a bit more knowledge about what all these such-and-such-biotics, and how each of them can help someone with a suboptimal gut. We’ll dive into the specific types of prebiotics and probiotics shortly and highlight which types of bacteria each will supply or help to enhance.

Rebooting The Gut With A Fecal Microbiota Transplant (FMT)

Posted in FMT on February 7th, 2017

Back in roughly 2007, I managed to acquire a clostridium difficile infection. It’s a really serious infection, usually preceded by antibiotic exposure, and it can often can lead to death if not treated. In my case, it mostly started out with flu symptoms, but gradually led to me being hospitalized for a few days due to loss of fluids.

Once being discharged from the hospital, I was prescribed flagyl to combat the c. diff infection. I did one or two rounds of that over a month or two, but unfortunately still tested positive for c. diff. at the end of it. Since the c. diff wasn’t really responding to flagyl, I was prescribed vancomycin, which at the time was one of the last lines of defence for most bacterial infections. I did several rounds of that over the course of a few more months, and thankfully eventually tested negative for a c. diff infection.

Unfortunately after all of that, I was left with a really fragile digestive system. Often I would have to go to the bathroom immediately after eating, or unfortunately would often have to hover near a toilet during the day just in case I had to go to the bathroom without much notice. I remember one road trip in particular where I knew I only had about 30 seconds to get to the bathroom, and had to immediately pull over on the side of the highway and run into a forest by the side of the road. Not a very pleasant experience, as anyone with intestinal issues can related to.

Over the course of the next few years, I went to doctor after doctor, trying to figure out what was still wrong with my gut. The diagnosis from most of them was ‘post infectious IBS’, basically some untreatable form of irritable bowel syndrome that happens after treating some other type of infection. In my case, the treatment for my c. diff infection, including all the rounds of antibiotics, led to the IBS.

I was told then to basically just accept it, since there’s not much they could do to treat it. And that’s basically what I did for the next four or five years.

The Microbiota

Up until recently, it was believed that the contribution of the bacteria in our intestines (the microbiota) was basically useless. But research over the past few years, thanks mostly in part to new 16S RNA sequencing technology, has led the realization that these bacteria are not only important, but may very well be implicated in many of the modern ‘diseases of civilization’ such as diabetes, obesity, IBS, Crohn’s, and even Parkinson’s disease.

Many people remember the Human Genome Project. It was an international effort to decode the human genetic code, which held the promise of a better understanding of human diseases. The hope was that through that effort, we could discover new and effective ways to treat and prevent modern disease. Unfortunately that project was basically a bust – it showed that we are all share roughly 99% of our genome, and that the remaining 1% didn’t really seem to do much to shed any light on disease.

As it turns out, in terms of sheer numbers, the bacteria in our gut have roughly 10 times the genetic material than our own genome. So it’s quite possible that when we went looking for the source of modern disease via the Human Genome Project, we went looking in the wrong place.

About a year ago I stumbled upon a service called uBiome that uses cutting edge 16S RNA sequencing technology to analyze a stool sample and determine the composition of bacteria in the gut. This technology has opened up huge new avenues of research over the last few years, and has helped the medical community start to unravel the mysteries of the microbiota and how each bacteria possibly influences health.

For example, most lean people contain Bifidobacterium as well as a bacteria called Akkermansia Muciniphilia – these are often absent in obese people. One role of Akkermansia is to form a barrier in the gut and stop foreign bodies from entering the blood. Lack of this bacteria likely contributes to what naturopaths call “Leaky Gut Syndrome”, where the gut doesn’t have tight junctions but instead allows foreign material to pass. Recent research into obesity has shown that at its heart seems to be an elevated level of lipopolysaccharides (LPS) in the blood which leads to systemic low-grade inflammation. Where does LPS come from? The cell walls of gram-negative bacteria in the gut. I could probably write several posts just about this ailment, but I’ll digress for the time being.

Since I knew I already had gut issues at this point, I thought it would be a good idea to do a uBiome test and see just what my gut looked like from a bacterial perspective. My first sample came back and showed that I was roughly in the bottom 14% of all people in terms of diversity (diversity is usually a good metric to evaluate the health of an ecosystem).

For the next five months, I set out to determine if I could improve my gut health mostly just by modifying my diet. I started taking prebiotics, which are beneficial fermentable fibers that some bacteria like to eat, and probiotics, pills that contain bacteria such as bifidobacterium. I also ate a lot of yogurt, and started making and consuming naturally fermented foods such as sauerkraut and kimchi. The current wisdom, at least in naturopath circles, is that this combination of foods and functional foods should have led to an improvement.

Each month during that period I did another uBiome sample, and took stock of any improvements (or lack of improvements in my gut). In general, my overall gut health didn’t change very much during those months, and my uBiome diversity bounced between 4% and 20%, with an average of about 10%. So basically despite my best efforts over a period of five months, I was unable to make any real impact in my gut diversity or any of my symptoms. It was time for another approach.

Fecal Microbiota Transplant

One of the most effective treatments for a c. diff infection these days is a fecal microbiota transplant (FMT). Basically you take the stool from a donor, extract the beneficial bacteria, and then transplant it into a patient with c. diff. The bacteria in the donor’s stool then immediately start to augment the bacteria in the patient, often re-establishing the defence mechanisms that normally protect against a c. diff. infection (in the case of a c. diff infection, it appears that most people become susceptible when an antibiotic disrupts the gut’s ability to generate secondary bile acids. These bile acids keep c. diff at bay, and the loss of the beneficial bacteria that convert primary bile acids into secondary ones cause c. diff to take hold and proliferate).

The cure rate for c. diff with a single FMT is about 90% – that’s far greater than any of the current antibiotic treatments such as flagyl or vancomycin. For three back-to-back FMT procedures, the cure rate is close to 97% – almost a home run as far as treatments go for any disease. The cure rate is in fact so high that during one study they had to stop it prematurely because it would have been unethical to continue to allow c. diff patients in the second arm of the study (those who weren’t having FMT) to continue to die when such an effective treatment was available.

While treatments for IBS and Crohn’s disease using FMT are still in their infancy (but they are being investigated), I was very convinced (based on all the research I had read to date) that since my gut problems started with a c. diff infection that perhaps a FMT would finally restore my gut to its previous healthy state.

Unfortunately here in Canada a person can only receive a FMT if they test positive for c. diff. Since I no longer do, I started investigating other options. I ended up stumbling upon a FMT clinic in Argentina known as the Newbery Clinic, and contacted Dr. Silvio Najt for an initial Skype consultation.

Dr. Najt agreed that given my history, FMT would likely be able to help. So I decided to book a trip to Buenos Aires for the procedure, and to enjoy a little bit of sunshine. I previously spent several months living in Buenos Aires, so I was really familiar with the city and the culture. If anyone is considering going to Argentina, I highly recommend it as it’s one of my favourite places that I’ve visited in the world.

The Procedure

Flying to Argentina

Flying to Argentina

I arrived in Buenos Aires after about 18 hours of travelling, and met Dr. Najt at the clinic a few days later. Starting then, I received five FMT procedures over a course of two weeks, each of which took about 60 minutes total from start to finish.

Each person reacts to FMT a little different, and I got to talk to a few other patients while there about their experiences as well. For me, I noticed I had a mild fever for a few days after my first procedure, which seems to be fairly common (you are after all injecting your body with a bunch of foreign bacteria).

Since bacteria like to munch on fiber, I switched to a high fiber diet roughly around the same time I started the procedures. Unfortunately for me, this caused a lot of digestive distress, both before and after the procedure. If I could go back in time, I probably would have upped my fiber content at this time, but not to the extent I did.

I didn’t really notice much of a change in terms of my gut health during my two week visit. I had some days where things seemed slightly improved, and other days where I seemed to spend a lot of time in the bathroom. Dr. Najt checked in with me every day or so, and kept an eye on how things were going and also helped to manage expectations. After the procedures were over, I hopped back on an airplane and headed back to cold Vancouver weather, with hopefully a new and improved gut that hadn’t shown itself completely yet.

The Results

Everyone I’m sure at this point is really curious to know what the end result was for me. It’s been roughly 10 months since I had the FMT procedure done in Buenos Aires, and it’s been pretty amazing just how much has improved since then.

In terms of my symptoms, I’ve gone from going to the bathroom 5 or 6 times a day to usually just once a day now. I used to have a lot of foods which would cause me digestive distress, such as almonds and grapes, neither of which cause me any issues anymore. In fact, there aren’t any foods at all now that cause me any issues. So in terms of my post-infectious IBS, I’m pretty confident in saying that I’m cured.

FMT Results

FMT Results

In terms of my gut diversity, uBiome shows that I’ve gone from roughly 10% diversity from before the FMT to 88% diversity as of my last test. Stated another way, I was in the bottom 10% of most people in terms of gut health, and am now in the top 12%. You can see the first five points on that graph from the period of time before the FMT, and the steady climb in diversity upwards since having it.

I suspect I’ll continue to have some positive gains over the next few months, but certainly the procedure seems to have significantly improved my gut diversity as evidenced by the 16S RNA sequencing data that uBiome does. I also have reacquired several important bacteria such as bifidobacterium longum and more recently, akkermansia. I’ve added a few more fiber sources to my diet recently, as well as resistant starch (both from whole foods), so I am interested to see if there’s even more improvement on my next uBiome test.


One aspect of my data that stands out to me is that despite five months of a eating very healthy diet (containing lots of prebiotics and probiotics, yogurt and fermented foods), I was unable to cause any significant improvement in my gut health (as measured by uBiome) or notice any improvement in my symptoms. So I would hypothesize that if a person has a very dysbiotic gut, FMT may in fact be the only long-term solution that leads to meaningful results, or at least the only solution that leads to results on a practical time scale. It’s like breaking your arm – you can rub as much polysporin as you want on it, but until someone sets the bone and puts a cast on it, it’s never going to heal properly.

Another aspect to take note of us that it has taken almost a full year to realize the full improvements from the FMT. So if anyone has recently had one or is debating having one, I think you should manage your expectations in terms of short term improvements.

Some people may question whether or not this procedure is safe. It’s a good question, even though FMT has an impeccable safety record so far. But the truth is that we are sharing bacteria with other people all the time – when we touch them, when we kiss them, and when we use public toilets. I would argue that this procedure, despite having an ‘ick factor’, isn’t really much different than needing a pint of blood in a hospital.

For me though, I’m happy I had the procedure done, and that after seven or eight years of having post-infectious IBS, am mostly cured at this point. Given the amount of diseases that are continuing to be linked to a disturbed microbiota, it’s good to know that my gut is now probably as healthy as its ever been. And in fact since my donor was breast fed and that I wasn’t, I may even have a healthier gut than I started with at this point.

Is The Body’s Metabolic Rate Tied To The Microbiota?

Posted in Research on February 7th, 2017

I read an interesting study recently regarding the effect of dieting on the microbiota in rats. What they found is that after the diet was over, the microbiota took nearly five months to recover to its previous state. During that period, the metabolic rate of the rats was basically reduced, forcing the rats to fatten up again if they ate the same caloric intake as they did previously.

This phenomenon, yo-yo dieting, is familiar to anyone who has tried to lose weight before. Despite your best efforts, it becomes increasing difficult to maintain your body at the reduced weight since the body physiologically wants to return to its previous weight.

More interesting is that these researchers managed to determine the cause, at least in the rats. A particular group of bacteria were diminished in the rats after dieting, and these microbiota had to do with steroid biosynthesis and flavonoid production. When these were missing, the rats metabolic rates (how much they burned in a day while at rest) dropped, leading to future weight gain.

So what does it mean? Well, it certainly seems like dieting can indeed lead to rebound weight gain. So vigilance is required for anyone who is actively trying to lose weight. It may take active effort for months after dieting just to maintain your weight while your microbiota sorts itself out. This is certainly an interesting line of research though, and it provides some promise regarding future treatments for obesity.

You can read more about the study here.

Welcome to The Happy Gut!

Posted in News on February 6th, 2017

Welcome to this site – the goal is to make this a great resource for everyone interesting in the microbiota and improving their health.