So, readers, I have fallen off the face of the Earth lately when it comes to maintaining this blog- it’s partly due to increased duties at work combined with illness (it’s a combination which pretty much guarantees the removal of all my spare energy), and it’s partly due to the fact that I’ve been devoting some energy to working on Project Cancer-Fighting Gut Bacteria.

Specifically, I’ve re-analyzed some data and made some new observations, and all this is going into an NIH R21 grant that I’m writing with my UCLA collaborator. The new planned work is, I think, better than what I had planned before with the team of people I had wanted to work with from not just UCLA, but Duke and Guelph as well. So the work is smaller in scope, in some ways, but should have an impact nevertheless if we manage to pull off the experimental work.

The next grant deadline that we plan to aim for is in the fall- so wish me luck. I’ll be working on this over my vacation in a couple of weeks.

Hello readers: I’ve come across an interesting article from my own home university, the University of Guelph! It’s entitled “Stress and the microbiome: linking glucocorticoids to bacterial community dynamics in wild red squirrels“, and it’s fascinating because (a) wild animals were used, responding naturally to their environments, and (b) it shows a direct link between levels of stress, as measured by faecal glucocorticoid hormones, and the microbiome, which controls so many aspects of one’s health. The paper comes out of the lab of Amy E. M. Newman.

The analysis is a little crude- the authors only looked at diversity of bacteria in faecal samples, not composition of bacteria to find which bacteria changed in abundance with stress- but it’s very clear that the overall diversity of bacteria in the microbiome of the squirrels analyzed in the study (via collection of faecal pellets) dropped when those pellets had higher levels of glucocorticoid hormones (which are an indicator of stress response).

What does this mean for you? Well, it’s clear from many studies that stress negatively impacts your health, and the alteration of the gut microbiome in response to stress probably happens in people as well as squirrels. This may be one more mechanism by which our psyche is connected to our physiological state via the gut-brain axis.

Hi everyone- so the interesting probiotic strain of Lactobacillus johnsonii (it has suppressive effects on lymphoma development in mice) that UCLA researcher Robert Schiestl is working with is being subjected to all sorts of studies. Dr. Schiestl himself wants to do some really interesting things with it, including human clinical trials, and I hope he finds the funds he needs to accomplish his fairly ambitious goals. I myself was trying to help him with this, and to also find funding to continue a project I had started in 2014. My project (Project: Cancer-Fighting Gut Bacteria) had the goal of figuring out one possible mechanism that this bacterium (and maybe other gut bacteria) might employ to affect human health. If I am right about the mechanism, it might be possible to design treatments that people who can’t tolerate probiotics, like chemotherapy patients who must avoid live bacteria, can take which might help them with some of the negative side-effects of chemotherapy treatments. Maybe. Even if I’m right, developing such treatments would take a long time, and of course the first step would be the experiments I and my collaborators were planning in the project.

I thought it might be possible to write an NIH R21 grant with the help of collaborators at Duke, the University of Guelph and with Dr. Schiestl’s help- but alas, there are three main impediments to this idea. The first is that I myself am not allowed to be PI on grants- my position simply does not allow this, and so in order for a grant to go forward, someone else has to be PI. Because this is a lot of work, I thought it might work if I volunteered to write the majority of the grant myself, and just get assistance with things like forms and submission deadlines- but unfortunately this situation isn’t working well with the long distances involved in this working group. The second impediment to my writing an R21 is that I am employed full-time as a researcher at the University of Guelph looking at environmental microbiology questions, and my employer is concerned that I’ll spend too much energy working on this project and not enough on her projects. This is a valid concern.  Thirdly, I am bipolar- and I find that if I try to push myself too hard and work too much, I break down. So I have to draw a line somewhere with how much of my spare time I can spend working.

So, the best solution to this problem is for me to find a position that allows me to focus on writing the grants I feel need to be written during my working days, and allows me to act as PI on those grants. This would solve a number of problems, and would also allow me to get credit for the ideas that are mine (a nice bonus). So until a situation comes along that allows me to be PI on the grant I’d need to write to fund it, Project: Cancer-Fighting Gut Bacteria is on ice.  This is a hard decision for me to make, since I have a deep personal interest in the project (my brother died of cancer in 2003, and loved ones of friends of mine have suffered through lymphoma chemotherapy treatments), and if I’m correct about the mechanism the finding would be quite important scientifically.  But I can’t afford to fund it myself, crowdfunding has not worked for me, and the only way I can write a grant and do it well is if I can focus on it properly- which means I need to be working as an adjunct professor, at the very least, and not simply a research associate.

I’m going to maintain this website, since it consistently gets a small number of hits and I hope the short pieces I write on probiotic bacteria will be useful to people seeking information. There’s a lot of hype and a lot of poorly researched articles out there- as I find interesting work I will continue to blog about it here.

Thanks for reading, and I hope you find something interesting on this site.

It had to happen sooner or later- I’ve come across the buzzword “psychobiotic” (meaning a probiotic, or live bacterium, which when ingested can help treat symptoms of mental disorders) online, and now in a publication (Psychobiotics and the gut-brain axis: in the pursuit of happiness, by Zhou and Foster, a review in Neuropsychiatric Disease and Treatment).  In the abstract, the authors state that a combination of probiotics, antibiotics, and fecal microbiome transplants (the latter is a drastic step to take indeed!) might be used to treat mental illness.

I think it’s a little early to be jumping on this particular bandwagon. While it’s clear that there are links between brain and central nervous system function and the composition of microbiota in the gut, it is likely that host genetics plays a part, and until we know which specific gut bacteria to remove or enrich for, and have therapies designed for these purposes, really it’s just shooting randomly in the dark. We still don’t know enough. The pace of research in microbiome studies is rapid, though- and I anticipate having real, designed therapies (clinically proven ones- do not forget this criterion, it is important!) in the next decade, if not sooner.

Another good paper to look at, if you are interested in the gut-brain axis, is this one, by Foster and Neufeld, published in Cell: Gut-brain axis: how the microbiome influences anxiety and depression. Most of the work they write about has been conducted in mice. I myself can’t find a single study on bipolar disorder and the human gut microbiome- if anyone wants to use me as a subject in such a study I’d be happy to volunteer! I notice links between what I eat and how I feel, both physically and psychologically. While it is possible that the food directly links these phenomena, it is also possible that food influences gut bacterial composition and activity, and then the changed microbiome has effects on my physiology and brain.

Merry Christmas, if you celebrate, and if you do not, I hope you have a nice day.

Hello, readers! I’ve been ill for some time and focusing on other projects, so unfortunately I’ve been neglecting this blog. I haven’t stopped my work on Project: Cancer-Fighting Gut Bacteria, and an NIH grant is in the works for that project with some collaborators of mine. If I had adjunct professor status at a university, that would make writing such a grant a lot easier, but alas, my funding situation is too precarious for me to get status at my home university, the University of Guelph, and unless funding comes through for my UCLA collaborator, there won’t be a chance for me to get this status at UCLA, either.

My UCLA collaborator, Dr. Robert Schiestl, has shared with me some of his ambitious plans for studying the Lactobacillus johnsonii gut bacterium that he’s already demonstrated has the ability to suppress lymphoma development in mice. I can’t tell you what the plans are, except to say he’d like to examine the possibility of this bacterium helping with a wide variety of diseases and syndromes linked to inflammation (and there are quite a number of these!). I am helping him seek funding for his project, partly because I want to see the trials go ahead, and partly because it would allow Dr. Schiestl to hire me and, if I am hired for long enough, I can get adjunct status at UCLA and take a lead role in the grant I’m trying to coordinate for Project: Cancer-Fighting Gut Bacteria.

Wish us luck! I wish I could tell you what is planned, as it is very exciting indeed, but I have promised not to.

I hope over the Christmas break, in between working on some other projects, to post a few more details of articles I’ve come across which I find interesting, and which you may find interesting, too.

Merry Christmas, if you celebrate, and if you do not, I hope you have a nice day.

Hello readers! I apologize for the lack of posts- I’ve been devoting my spare time to a novel I’ve been writing, as well as a number of grant applications. One of them is for an NIH R21 for Project: Cancer-Fighting Gut Bacteria.

Earlier this week I experienced a bout of food poisoning, and at the same time an intensification of symptoms associated with my bipolar disorder. This made me think of the articles I had been posting on this site and once I recovered, and looked through my notes for Project: Cancer-Fighting Gut Bacteria, I realized that I needed to find more articles on probiotics and whether they establish in the gut, as well as whether they have any beneficial effects on diseases of the gastrointestinal tract, and how they work.

The results of this search, which I conducted over several hours tonight, have been fruitful! I share with you the URLs for three of the most accessible articles I have come across.

First of all, an older article but a good one that’s been cited more than 400 times: Probiotics: determinants of survival and growth in the gut. Essentially, the take home message is that, while probiotics can have beneficial effects on controlling things like diarrhoea, and can survive transit of the stomach into the lower GI tract, there’s no evidence they actually establish in the intestines- they seem to exert their effects while passing on through. This suggests that in order to get a beneficial effect from probiotics, you might have to keep taking them consistently.

Here’s a newer article on the same subject: A Meta-Analysis of Probiotic Efficacy for Gastrointestinal Diseases. This article summarizes research from a lot of other articles, all studies of the effects of probiotics on different diseases. The take-home message is that, for most probiotic bacterial strains and diseases, taking probiotics can help- but there are some diseases that are not as well treated, and some bacterial strains that are less effective. Quoting from the abstract, “Six of the eight diseases: Pouchitis, Infectious diarrhea, Irritable Bowel Syndrome,Helicobacter pylori, Clostridium difficile Disease, and Antibiotic Associated Diarrhea, showed positive significant effects. Traveler’s Diarrhea and Necrotizing Enterocolitis did not show significant effects of probiotcs. Of the 11 species and species mixtures, all showed positive significant effects except for Lactobacillus acidophilus, Lactobacillus plantarum, andBifidobacterium infantis.” The last sentence is important, since L. acidophilus is typically found in yogurts, and if this is the only strain in your probiotic preparation, or the main strain, it might not be as effective as you’d like against a disease. There still may be other health benefits, just not necessarily control of disease.

A very useful article with a lot of really nice figures that explain in detail how probiotic bacteria exert their effects on you (it might be a bit too technical, but it is open access so there’s no harm in taking a look) is this one: Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. It talks a bit about the gut-brain axis, which is of particular interest to me (especially this week, given my health issue from earlier), and it also talks about how gut bacteria can affect your immune system. There also is a bit of discussion of how dietary compounds (like histidine, glutamate, and dietary fibre) lead to the production of compounds that affect your metabolism (like short-chain fatty acids (important for colon health), gamma-aminobutyric acid (GABA, a neurotransmitter) and histamine (influences inflammation and immune responses).

I apologize for being absent from this blog for so long and I hope you enjoy these articles- all are or should be open access, but if you have problems accessing any of them write to me and I will see if I can help you find a PDF.

Several of my friends suffer from fibromyalgia. I wondered if there was a possible link between the fatigue and muscle pain (myalgia) they suffer, and I found this interesting article from the Journal of the American Medical Association, authored by Henry C. Lin: “Small intestinal bacterial overgrowth: a framework for understanding irritable bowel syndrome“.

Now, bear with me, this article is not just about irritable bowel syndrome (IBS)- in the abstract it mentions, at the very end, how the distinction between small intestinal bacterial overgrowth and IBS may focus on a specific set of symptoms that exclude fatigue and muscle pain, while diagnoses of chronic fatigue and fibromyalgia are focused mainly on these symptoms. The authors of the article suggest that this distinction may be academic- an artefact of medical training- and put forth the idea that maybe all these various symptoms can be traced to a single cause, namely, gut dysbiosis (here specifically focusing on small intestinal bacterial overgrowth).

This is a hugely important and interesting idea, and taken along with the article I have mentioned in my preceding post, a review of the gut-brain axis (where changes in gut microflora can result in psychological changes), gut dysbiosis (unhealthy gut microflora) may contribute not only to symptoms like muscle pain and fatigue, but to mood disorders as well.

The obvious question for people suffering from these symptoms is, how can I fix my gut microbiome, if it might be unhealthy? This is a hugely important question. Right now research is focusing on finding “good guy bacteria” that can help maintain healthy states, but it’s important to remember that it’s not enough to simply take a probiotic- if you take bacteria and add them to an environment where they can’t grow and establish, they will simply pass right on through your intestines without making much of a change. It’s known that factors such as what you eat, how much and when you exercise, how much and when you sleep, and if you’ve become sick (food poisoning, for example) will all affect the composition of your gut microflora. Establishing a healthy microbiome will probably require that you follow a doctor’s advice with all these factors and do so in a steady, long-term fashion- not that you simply take a probiotic supplement or eat fancy bacteria-containing yogurt.

[UPDATE: There are a TON of quack websites out there which claim to have miracle diets or cures for small intestinal bacterial overgrowth (SIBO): if you read anything like that, stop! It’s fake! It won’t help and might harm you. SIBO treatments have to be custom-tailored for each person. Please take the above cited article and this one to a real medical doctor, not a naturopath, and if you look at websites make sure they are from reputable, accredited medical schools.]

In future, I am hoping that work based on ideas I have might help people whose gut microbiomes are unhealthy and, for whatever reason, can’t take probiotics, or in whom probiotics are not effective (probably because the gut environment is hostile to those added bacteria). Right now I am focusing on an interesting strain of Lactobacillus that helps fight lymphoma, but the lessons I learn from this organism may help me study ways to use other gut bacteria with different kinds of effects on human health, to help a lot more people.

Hello readers! I have downloaded the most interesting- and high quality- review I could find on links between gut bacteria and brain functioning/mood, and it is can be found via this link: “Gut-brain axis: how the microbiome influnces anxiety and depression”. The journal is Cell and the review is written by Jane A. Foster and Karen-Anne McVey Neufeld, both of McMaster University.

I haven’t had time to read all the articles listed in Table 1, which is an outline of different kinds of studies done with mice and the psychological effects of changes in gut microbiota. However, while I plan to discuss these works in more detail in the future, I’d like to direct your attention to Figure 1 in this article: it nicely sums up the different, and interconnected, effects that changes in gut bacterial community composition (or, changes in your gut microbiome) have on your body, including your brain. A change on one partner (your body, or your gut microbiota) will have feedback effects on the other partner, which then leads to additional changes to the first partner.

Figure 1 caption (I’ve added additional notes in italics): Bidirectional (two-way) communication between gut microbiota and components of the gut–brain axis which influence normal homeostasis (the state your body is in when you are healthy, and the systems which maintain that state) and may contribute to risk of disease. Alterations in gastrointestinal (GI), central nervous system (CNS), autonomic nervous system (ANS), and immune systems by microbiota may lead to alterations in (a) fat storage and energy balance (or, you may find yourself prone to changes in weight); (b) GI barrier function (the GI barrier keeps your gut from “leaking” and allowing in antigens that cause inflammatory responses, which if unchecked can lead to disease states like colitis); (c) general low-grade inflammation (GI and systemic, or body-wide); (d) increased stress reactivity (or you are more sensitive to stressors); and (e) increased anxiety and depressive-like behaviors. Each of these mechanisms is implicated in the pathophysiology (disease physiology) of mood and anxiety disorders.

I apologize for not having an explanation of this article ready for consumption today, but please stay tuned for it in coming weeks.

Hello, blog readers! I apologize, for I have sadly neglected you- and I failed to update this blog with summaries of the many interesting articles that have crossed my desk. I have been taking courses in bioinformatics, and travelling- and one of my travels took me to Duke University where I met with one of my collaborators in person for the first time.

While I was there, I received email notification that the small grant I had applied for in June was not going to be funded. I hadn’t expected it to be- only four of those grants are funded out of however many applications they get, and so it is a very competitive program. My co-PI and I still await the reviewers’ commentary on our application.

However, all is not lost- it’s been decided that my Duke collaborator will help me apply for an NIH R21 grant, which would allow everyone (not just the Canadians) to be paid from the grant. My Duke collaborator and I sat down that afternoon and put our heads together, and came up with a marvellously scribble-filled page of notes for the project we think we should do- and it is bigger, better, and if funded will be an amazing piece of science! I am slowly putting all our thoughts into words- slowly because I am still waiting for feedback on our first grant application, which will inform this one, and also slowly because the deadline for this program is in October, though I believe we can apply earlier than that.

So my trip to Duke was not simply an exercise in networking, it was very fruitful and I’m so glad that I was able to do that! Stay tuned for more updates on the R21. Again, these are competitive grants, and it’s possible our application won’t be funded- but it won’t be for lack of our trying, or doing the best job we possibly can.

I hope to post a few more summaries of interesting research articles in the coming weeks- it’s been hard to find the time, as I am responsible for putting together this R21, other personal writing projects have caught my attention and, as always, I still have a full-time job that I have responsibilities toward. Still, every week new and interesting research on the subject of gut bacteria and how they affect their animal hosts is published, much of it not very accessible to the general public. I’d like to share more of these articles with you in hopes that you find the work as interesting and informative as I do.

Hi- I’ve been writing articles for fun for The Conversation, and enjoying the attention those get. I’ve neglected to post much to this blog because of that, but later today or tomorrow I plan to contribute a new post describing a paper from Neuroscience in which links between gut bacterial composition and the functioning of the mouse nervous system are described. It will be a very interesting read!
I’ve also written an article on probiotic bacteria for a website called, but that hasn’t been posted- the website’s maintainer has faced some difficulties recently and hasn’t had time.
Here are the four articles I’ve written so far for The Conversation, and I hope you find them of interest.
How gut bacteria affect your immune system and response to vaccines –
How soil bacteria and fungi can help plants grow (this one was the first and it was not well edited- it needs a bit of work) –