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Wednesday, December 23, 2015

Recipe hacks for good gut microbes

My time is devoted to learning and writing about the science of gut microbiota. As fascinating as it is to go deep into the mechanisms of gut-brain communication or how human versus bacterial genes contribute to obesity, I've been thinking a lot about the practical side of the science: how can I build what I know into my own life? What are the actionable items from this science?

Diet is a powerful way to affect the microbiota -- this much is clear. So when I've been making meals, I've been trying to hack them in ways that are good for my gut microbes. Here are three recent recipes:

Three-day salsa
Fermented foods deliver live bacteria to your gut, with possible beneficial effects on health.

Cauliflower 'rice' with ham
We still don't know the effects of processed meat on the gut bacteria specifically, but the best available evidence supports bulking up on fibre and eating processed meat in small quantities.

Easy gingerbread cake
You're going to eat something sweet from time to time, especially around the holidays. Spelt flour and prunes boost the fibre content of this cake, giving your gut bacteria something to chew on.

Merry Christmas!

Monday, April 20, 2015

A Microbiome Three-Conference Summary

During the month of March, I've been pleased to cover three great microbiome-related conferences for the Gut Microbiota for Health website. I heard about interesting things happening in the field -- research both deep and broad -- and talked to scientists and clinicians from around the world.

Here are the conferences I attended:

Keystone Symposium - Gut Microbiota Modulation of Host Physiology: The Search for Mechanism

Gut Microbiota for Health World Summit 2015

Experimental Biology 2015

It's hard to summarize the mass of information from these conferences, but here are some of the important messages I heard about gut microbiota:

"Lactobacillus spp Sauerkraut 1" by A doubt - Own work.
Licensed under CC BY-SA 3.0 via Wikimedia Commons -

The gut microbiota are constantly changing; in a single person, composition varies from day to day and over the course of the day.

Diet has a huge impact on (a subset of) the microbiota, with effects on long-term health; the impact of fibre is among the hottest areas of investigation.

Bacterial viruses (bacteriophages) are an important part of the gut community, and may have a role in diseases like Crohn's and AIDS.

Bacterial species are often interesting to note, but it's the metabolites they produce that may be doing the key work in the body.

The immune system is extremely sensitive, responding to slight shifts in the gut community and maybe even suffering long-term 'scarring' from environmental factors.

Clinical trials with therapies (e.g. fecal microbiota transplantation or probiotics) are useful, but it's even more important to investigate mechanisms that are making them work, so we can match therapies to patients with perfect precision.

So far, the established, concrete clinical applications of microbiota research are few (for example, fecal microbiota transplantation for C. difficile), but the intangible clinical applications are many!

I also talk about these three conferences in this podcast interview with the great guys at the American Microbiome Institute.

You can find Storify summaries of the live tweets from Keystone and Experimental Biology here:

Keystone Day 1
Keystone Day 2
Keystone Day 3
Keystone Day 4

Experimental Biology Day 1
Experimental Biology Day 2
Experimental Biology Day 3
Experimental Biology Day 4

Get in touch if you want to know more details about the science!

Tuesday, July 1, 2014

What's on the menu at your local long-term care facility?

I recently came across the work of Paul O'Toole, of University College Cork (in Ireland). He works with the Alimentary Pharmabiotic Centre, which focuses on developing "bench-to-bedside solutions focusing on gut health". O'Toole was interviewed about one of his recent presentations here.

Some of O'Toole's recent work has to do with the relationship between diet and gut microbiota in elderly people. I recently wrote an article about nutrition for seniors that piqued interest here in Canada, so O'Toole's major findings are really interesting to me:

- The setting where an elderly person lives appears to determine his/her gut microbiota: based on microbial species in fecal samples, scientists could predict which seniors lived in the community, a day-hospital, a rehab setting, or a long-term care facility

- The difference in gut microbiota in each setting could be because of different diets

- In general, seniors living in the community has diverse gut microbiota, and seniors in long-term care had less diverse microbiota

- Low-diversity gut microbiota correlated with poor health: sarcopenia (muscle loss), inflammation, and even lower cognitive function
Source: Wikimedia Commons (Siobhan from Upstate New York)

Like any human research, it's not easy to tease apart cause and effect here. This issue of causality has been controversial on at least one other paper that O'Toole co-authored. But the bottom line is that seniors in care facilities have a less diverse microbiota and poorer health.

It could be the case that by the time a person is ready to go into long-term residential care, he/she is already naturally in a state of declining health, regardless of diet. But we have converging evidence from other places that diet can indeed affect health through the microbiota. The other major possibility is more intriguing: what if the poor diet of a senior in a long-term care facility was the thing that caused poorer health from the day they entered? This isn't so far-fetched, as those who study geriatric populations (like Keller, below) will tell you.

I, for one, wouldn't be so keen to support an elderly parent going into a care facility if the menu was going to guarantee a health decline.

The problem would seem to have such a simple solution: change the menus in these care facilities. But I doubt it's as easy as it looks. There are all kinds of social and cultural factors to consider when creating menus, not to mention the pressure of keeping down costs. Dr. Heather Keller at University of Guelph is knowledgeable about some of these factors.

A word to the wise here, if you happen to be checking out the menu at your local long-term care facility: macaroni and cheese won't cut it. Elderly folks need protein, protein, and more protein.

Tuesday, May 28, 2013

Two tales of gastric bypass surgery

This story appeared today from The Canadian Press:

Mom's obesity surgery may help her children

It reports on a study that followed kids' risk factors for obesity. Children who were born to an obese mother before she had weight-loss surgery were heavier, and had higher risk factors for heart disease and diabetes, than children born to that same mother after surgery. Researchers say it was because obesity causes differences in the activity of certain genes. Not that obesity affects the genes themselves, but how the genes express themselves.

The story is fine by itself. Rather well written, in fact. (Bonus points for great quotability go to co-author Dr. John Kral, who said fetuses are "differently marinated" depending on the weight of the mother.) And everything would be hunky dory were it not for this item, which was covered by Reuters two months earlier:

After weight-loss surgery, new gut bacteria keep obesity away

This one explains exactly how gastric bypass surgery helps people slim down. Researchers found that it may not have to do with going under the knife, but rather, with how the surgery changes the patient's gut bacteria. (The study was done on mice, and as a result, controlled for nearly everything; control group mice were even given a "sham" surgery.) The study raised an important question: might it be possible to skip surgery, and achieve the same effect by altering gut bugs through diet or another means?

These stories were two separate entities, presented weeks apart. But taken together, here's what I gather:

1) A mother's gastric bypass surgery helps change a baby's gene expression and makes him or her healthier for life

2) Gastric bypass surgery might not be necessary because what matters is the change in bacteria that occurs after the surgery

So if you were a woman of a high body weight who planned to become pregnant, wouldn't you want someone to have raised the connection between these two studies? Maybe you read the news today and have become convinced that gastric bypass surgery is the best way forward, even with the risks it presents. And your appointment to discuss it with your doctor is tomorrow.

But maybe you could have had other options.


The fact that no one communicated the connection between these studies is a huge oversight. I'd even argue that it is bad for scientific progress. Science is about converging upon the truth with different studies conducted under different circumstances. So why are we still presenting science studies without context or analysis, as individually-wrapped peppermint candies?

Let's give everyone the benefit of the doubt in this case and say it's because the person assigned to cover the study wasn't aware of any other relevant studies. Sure, the scientists this person interviewed are supposed to have told him or her about the context. But it's not actually a scientist's job to be aware of the news coming out of other labs at any given moment. It's the journalist's job to be informed in real time.

This is a strong argument for assigning health and science stories to those who make it their full-time mission to keep abreast of a certain area of health and science. That is to say, specialist journalists. (Luckily there are several great people, including Rob Steiner at U of T, who are working to create a new generation of specialist journos that will provide content to newsrooms that are operating on a skeleton staff of generalists.)

These two studies are just one example of something I notice all the time. Other specialists could probably cite examples from their own fields. The point is, news is set up for these obvious failures to connect the dots. But we need to work toward changing that. It's only fair to that woman - a future mother - signing the surgery release form at this very moment.

Thursday, May 2, 2013

Autism and gut bacteria: The vax. Er, the facts.

When you do an internet search for "autism" and "vaccine", you open the can of worms that was the claim that MMR vaccines caused autism. That fraudulent research and the conniving scientist behind it, Andrew Wakefield, have now been discredited. (For more on that, see the dedicated chapter in the book "Bad Science" by M.D. and writer Ben Goldacre.)

But lately in the news, we came across the words "autism" and "vaccine" in the same sentence again. As in these headlines:

Vaccine developed at U of G could help in battle against autism

Vaccine developed to fight gut bacteria and autism symptoms

First vaccine against autism-associated bacterium Clostridium bolteae

Just how did those two words end up together again? It piqued my interest.

The word vaccine is particularly suggestive. Because what we do know about the cause of autism is this:

(1) There is definitely a genetic component
(2) There may be an environmental component, but scientists don't agree on what it is

A vaccine would not address genes, of course. It would address one of the environmental components thought to cause the condition. But... hold on, if we're not sure what the environmental causes are, how can we take a vaccine and say it addresses that environmental cause?

With that question in mind, I approached this research, which came from the chemistry lab of Dr. Mario Monteiro at the University of Guelph.

I took the step (as always) of reading through the original research paper in the journal Vaccine (in press as of early May, 2013).  Ahem... that was clearly one more step than most of the reporters who produced articles on the topic (bless their time-strapped hearts). See, anyone who said there was a vaccine obviously didn't read or understand the paper. Because in the article, there is no vaccine.

Here are the facts:

A team of chemists has examined the cell walls of a kind of bacteria (Clostridium bolteae), and have determined that the bacteria can provoke an immune reaction in rabbits.

That is all.

The researchers say their knowledge could be used to develop a vaccine for human use (i.e. they now have a vaccine target), but they did not yet create the vaccine themselves. Contrary to what  pretty well every mainstream news article has reported.

Moreover, the facts in this article are padded with the stuff about autism that, given the context, seems absurdly off topic. They took their discovery of making the immune system of rabbits react to a bacteria, and they said, "Hey, some children with autism also have this bacteria in their guts. Maybe we could develop a vaccine against this bacteria and give it to them. And the bacteria would go away. And maybe so would their autistic behaviours."

Do I need to say it? That is not sound scientific reasoning. It's like saying:

"Hey, some children with blonde hair also have this bacteria in their guts. Maybe we could develop a vaccine against this bacteria and give it to them. And the bacteria would go away. And maybe so would their blonde hair."

To me, the paper is about developing a knowledge about a species of bacteria. At most, the discussion section should have mentioned that this particular bacteria may be found in the digestive tracts of some children with autism.

I'm not really sure why they picked on this species of bacteria, in fact. There is no scientific consensus that C. bolteae is special to the guts of children with autism. Some studies have been done comparing the bacteria in the guts of children with autism to that in non-autistic children, and even though some patterns are emerging, there are no bacteria that reliably distinguish one group from the other. This species of bacteria alone is surely not the "environmental cause of autism" that has been eluding scientists for decades. The researchers do make a case for why they chose C. bolteae, but to me their choice seems questionable, given the conclusions of the papers they cite.

Now, I do think that the connection between autism and gut bacteria warrants more research. (See this episode of David Suzuki's TV show, The Nature of Things.) I'm not dismissing it wholesale. It's just that this paper goes beyond what the empirical evidence shows - both in the peer-reviewed journal and in the media.

The upshot (yep, pun intended): the word "autism" should not be appearing with the word "vaccine" here at all. That's because the word "autism" should not appear at all, and the vaccine is still a dream. The headlines should read something like:

"Scientists may develop vaccine against species of bacteria with unknown importance".

Only, then they wouldn't be headlines. Hmm, see?? Pequegnat, B., Sagermann, M., Valliani, M., Toh, M., Chow, H., Allen-Vercoe, E., & Monteiro, M. (2013). A vaccine and diagnostic target for Clostridium bolteae, an autism-associated bacterium Vaccine DOI: 10.1016/j.vaccine.2013.04.018

Tuesday, March 5, 2013

What expectant parents need to know about baby's gut bacteria

Expectant parents, tell me this:

If there was a thing you could do for your child that might decrease his or her chances of being obese, suffering from asthma, or developing type 1 diabetes later in life (and possibly more)... how hard would you try to do it?

Well, there is a thing. And that thing is protecting the little one's gut bacteria, right from day one. 

When I was expecting my daughter, I was already a full-on gut bacteria geek. Instead of reading What to Expect before bed, I was downloading studies on the gut bacteria of newborns. Oddly, the topic was nowhere to be found (outside the scientific literature) in my pre-baby immersion experience. I don't remember a single mention in the parenting books, blogs, prenatal groups, or even my medical professionals.

Luckily for all the babies yet to be born, that silence around gut bacteria will definitely change over the next couple of years.

How do I know? Because the science that's already out there says that gut bacteria is highly relevant to both labour and newborn care. Health outcomes later in life may have everything to do with those couple of days leading up to birth, and with the birthing process itself. It's not just an exercise in getting the baby out. It's the challenge of getting the baby out with good gut microbiota intact. This microbial garden is so important that microbiologists are starting to think of it as the baby's "forgotten organ". Not sure about you, but I would certainly want my baby delivered with all of its organs included.

Photo source:

In a nutshell, these are the things that can have an impact on baby's gut microbiota:

1) Mom receiving antibiotics before and during labour
2) Baby born by caesarean section
3) Baby breastfeeding
4) Baby receiving antibiotics early in life

Even in the past year, researchers have started to put more empirical data behind these. A few of the above started out as mere theories, but now there is evidence for each one of the four factors.

One recent Canadian study that investigated factors 2 and 3 above was called Gut microbiota of healthy canadian infants: profiles by mode of delivery and infant diet at 4 months, published in the Canadian Medical Association Journal. With 24 subjects, the study is big enough to be interesting, though small enough to warrant continued research.

The study was basically a snapshot of gut bacteria at a single point in time - 4 months - along with information on the infants' birth and health histories. Researchers found that all kids had certain bacteria in common (e.g. Bifidobacteria), but there were some important differences:

Vaginal birth vs. Caesarean section

Certain bacteria were "underrepresented" in all infants born by c-section, as compared to those with a vaginal birth: those of the genus Escherichia–Shigella. And one entire phylum of bacteria (Bacteroidetes) was absent from the c-section babies.

Elective caesarean section vs. Emergency caesarean section

Here is an interesting one - the researchers found that the gut bacteria of those born by elective c-section had the least richness and diversity of all groups. Leaving aside the question of whether low richness and diversity is a bad thing, it could be that elective c-sections result in different intestinal bacteria than emergency c-sections, which happen after a woman's body has initiated labour. Researchers are intrigued, but not yet sure why this could be the case.

Breastfeeding vs. Formula

A difference here should be no surprise, since breastmilk is full of great bacteria. Even the fancy probiotic formulas can't do exactly the same job. The breastfed babies had significantly higher numbers of 2 families of bacteria (the eloquently-named Peptostreptococcaceae and Verrucomicrobiaceae). Formula-fed babies had more richness and diversity, meaning that the breastfed babies had fewer overall species present and that certain species tended to dominate in the gut. Notably, babies on formula harboured more C. difficile.

The data in this study is descriptive, and the researchers left out the weighty question of what kind of intestinal garden is better and what's worse. See, we don't yet know what the ideal gut should look like at 4 months, so we don't yet know what a poor gut looks like, either. All 24 infants were healthy, so in some sense the data all describe the range of normal. But judging by other research on health outcomes, it's fair to say that whatever the vaginal birth and breastfeeding do to the babies' gut bacteria, it's a good thing.

I was happy to see this study reported so widely in the media when it was published in February. There were several great articles on it, including one by Paul Taylor in The Globe and Mail.

I did shake my head, however, at one misleading line that was meant as a caution:

"Canadians seem to be opting for c-sections in increasing numbers. "

As I outlined in a series of tweets, the (limited) data show that women are not at all "opting" for c-sections.

The increasing c-section rate is likely because of more emergency c-sections - which has to do more with the decision-making of surgeons rather than mothers. A study right here in British Columbia, a place with one of the highest c-section rates in Canada, found fewer than 2% of those surgeries were a result of maternal request. (Incidentally, collaborative maternity care in B.C. has been shown to reduce the number of c-sections.) 

There's one other thing I have to address with this study. That's the anxiety of parents who have already birthed their bundle in a situation where things weren't exactly optimized for great gut bacteria. I know more than a few people in that boat.

Not to worry. There are things you can do later in life to keep your little one's garden growing well. Some of my other blog entries explain what these are (here and here, for example).

And if you are a parent-to-be who really really hopes you can protect that baby's gut bacteria on the important day that it decides to enter the world, I want to share the best piece of wisdom I got before the birth of our little girl: "Labour is like a box of chocolates. You never know..."

Which means, you can't control everything all the time. Least of all a brand new, squirmy human, a mother's wonderful and wise body, and teams of midwives and doctors and nurses. You may indeed end up having a c-section and unable to breastfeed. But simply by being aware of the factors that affect baby's gut bacteria, you can take steps to nurture it as best you can.

Saturday, December 29, 2012

Book Review: Wheat Belly is a bestseller, but what's the science behind it?

If a doctor writes a book in the forest...
Wait a minute, that's not right.

If a doctor writes a book about health... is it science?

This is the question I had in mind while reading Wheat Belly. When a physician like William Davis, MD, takes time out of his (no doubt) busy schedule to write a health-related book, ideally he has taken the time to  get familiar with all the scientific literature on the topic. This may be easier for doctors than for some other writers, as Davis may have had the benefit of hearing research summaries at conferences, or having literature reviews arrive on his desk with the daily mail. Add that to years of clinical experience, and you have the potential for a pretty compelling argument on a health issue.

But what if, instead, a doctor seems to have spent years giving a certain piece of unusual clinical advice about a dietary change. And he has had such great success with patients who follow that advice that he goes looking for science to explain why it works. He scraps together a few studies that he thinks are relevant, connects some dots, and writes a book. What then?

Interesting, but not necessarily science.

So here's the heads up: Wheat Belly is an example of the latter. Though Davis, a cardiologist, has written a very interesting book with a timely message, you should know that it is not strictly based on science. Meaning: there is no thorough review of the evidence for his claims about the ill health effects of wheat.

Case in point: the glycemic index stats he cites are from an article published in 1981 - and he repeats again and again that the study found a greater blood sugar rise with "whole-meal" bread than with white bread, even though - ahem - a fair amount of glycemic index research has been done since, and a quick visit to almost any diabetes association website will confirm that whole wheat breads (for the most part) have lower glycemic indices than white breads. Davis gives a few nods to how his claims fit in, or don't fit in, with the advice of professional bodies. But he doesn't present a complete picture of why and how science shows that eliminating wheat from one's diet is a good idea.

One other reason I know he hasn't done a thorough review? I know about another body of science relevant to the topic, which gets little to no mention in Davis's book. That's the science to do with gut bacteria. But more on that after I summarize the book.

The point of the book is that it's bad to eat things that spike your blood sugar - i.e. things with a high glycemic index (GI). Apparently wheat spikes the blood sugar more than you'd expect - the oft-cited study found whole grain bread had a GI of 72, while a Mars bar had a GI of only 68 - and therefore we should eliminate wheat.

It follows that we should eliminate all things that spike blood sugar. Davis advocates this. So properly, the book should be called "Carb Belly". (Of course, the arguments against carbs have been well-explored in books that promote the Atkins diet, Paleo diet, Specific Carbohydrate diet, etc.) But Davis says the one carbohydrate that people have the most trouble eliminating is wheat. Hence, the name Wheat Belly.

Here's what's in the book:

Part 1:
Davis explains how wheat strains have changed with hybridization and how modern types of wheat affect us in unprecedented ways.

Part 2:
Davis describes wheat's "head-to-toe destruction of health": (1) the addictive properties of wheat that can influence behaviour and mood, (2) the way wheat triggers blood sugar and insulin extremes, which lead to visceral fat accumulation, (3) how intestinal permeability triggered by a protein in gluten may be responsible for the rise of autoimmune disorders and digestive disorders, (4) an argument that wheat may cause type 2 diabetes, (5) an explanation of how wheat affects the body's pH, resulting in an "acid-rich situation" and that promotes osteoporosis, (6) wheat's promotion of AGEs, which signal aging, (7) how wheat leads to heart disease by increasing triglycerides that turn into atherosclerotic plaque, (8) how the immune system's attack on nerve cells results in cerebellar ataxia and brain fog, and (9) how increased levels of insulin, and an immune reaction to gluten, can show up as acne or skin rash.

Note that for most of these claims, Davis's evidence is in the realm of the "theoretically possible." As far as I can tell, the science actually addressing these claims is weak. The studies conducted on humans where all else is equal, except the inclusion of wheat in the diet, are rare. Making his claims premature at best.

Part 3:
He talks about the "how to" of eliminating wheat and other carbohydrates. The book includes menus and recipes for low-carb eating.

I have to jump in here and say, "What about the gut bacteria? Don't they get any consideration?" Because here are just some of the studies that may be relevant to the issue of eliminating wheat and/or all carbs:

- Evidence on how gut bacteria influences carbohydrate digestion throughout the lifespan
- Evidence on how bacterially-pre-digested white bread (a.k.a. sourdough) is metabolized differently from other breads
- Evidence on how fibre (prebiotics - known for their promotion of good gut bacteria) stimulate the immune system and increases the bioavailability of nutrients

He missed a few things. But can we really knock Dr. Davis for proposing a low-risk treatment that seems to work like magic for a host of health problems? Can we truly fault a compelling book that's convinced a lot of people to do something that clearly helps their health?

I think it's a good thing that he's written this book and that it's sold so widely. I'm biased of course, having been on a gluten-free diet for five years or so. It also doesn't escape me that it took a lot of bravery for him to so emphatically convey this message in a world that is very wheat-centred.

So yes, Davis has perhaps inspired many people to initiate a positive change for their health by penning a bestselling book with lots of media coverage. But by putting together a misleading scientific grab-bag of reasons for convincing people to make this change, he is assuring that they never fully understand what caused their health problems in the first place. They put on a bandaid without understanding what might have caused the wound.


...pretty well tell the same story as these: