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.

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) –

Just a short blurb regarding this new Nature Communications article regarding differences in the gut bacterial communities (microbiomes) of people living different lifestyles. In this study, microbiomes of people living in different ways, from the following groups: (1) the Matses, a remote hunter-gatherer population from the Peruvian Amazon; (2) Tunapuco, a traditional agricultural community from the Andean highlands; and (3) residents of Norman, Oklahoma, a typical US university community that serves as a comparative population following an urban-industrialized lifestyle.

What was found that, in support of prior work, the rural community microbiomes had greater richness (number of different organisms) than the microbiomes of people in the urban population sample. There were a variety of differences in the compositions of the microbiomes that meant it was possible to predict what group a person came from based solely on their gut microbiome. Perhaps even more interesting, though, is that the Matses people had strong signatures of variants of the bacterial genus Treponema that were present to a lesser extent in the Tunapuco people, and largely absent from the urban sample.

If you’ve heard of Treponema, you’ve probably heard of it in its context as a pathogen: species of this genus can cause different diseases, including syphilis. However, the Matses people sampled were perfectly healthy, and the signatures of Treponema found in them are more closely related to symbiotic gut bacteria in creatures such as termites than they are to the pathogenic species.

What are these newly discovered varieties of Treponema doing? Functional gene analysis between the microbiomes of the three groups of people showed differences in the abundances of some gut bacterial genes, associated with things like metabolism of carbohydrates.  Might these bacteria belong to a long-lost group of “good” gut bacteria that a typical Western lifestyle has eradicated? It will be interesting to see if there is work following up this study to learn more about these bacteria.


I spent some time putting together drafts of two articles that may be of interest:

1. How CRISPR-Cas systems (combinations of RNA and proteins) can be used as very precise tools to target and kill specific bacteria of interest in a mixed community, leaving non-targeted neutral or “good” bacteria alone. These tools require further development before they can be used in medicine, but hold so much promise! This article was written for the website The Conversation.

2. How some isolates of probiotic bacterial strains originating in the human gut can affect the lining of your intestine- in the study I reference, some of the isolates (notably Bifidobacterium bifidus) that were found were able to actually repair damage done to the gut lining by a molecule known as tumour necrosis factor alpha. This is exciting news! This article was written for the website

I will post a link to each article as they become publicly available.

So, getting the materials I need to conduct the follow-up tests I have planned for study of the Lactobacillus johnsonii lymphoma-fighting strain is proving to be more challenging than I had anticipated. I think this could be smoothed out by liberal doses of cash, but of course, everyone’s research project could use more cash. I will try again to try and find funding sources for this sort of work- all the ones I had looked into before now ruled me out, because I am Canadian or not a faculty member, or ruled out my being able to work with UCLA, because it is a US institution. You’d think with NAFTA this sort of thing would be easier! Business grants care less but need a marketable product, and this is for basic research. Still, perhaps there will be a funding source I haven’t come across yet, or perhaps I will find a collaborator that can help me.

People wonder why scientific research is so slow- half the time we have is spent chasing money sources to do the actual work, a quarter of what is left is spent trying to train other people how to do the work properly, and then half of what’s left after that is spent trying to solve lab problems, like malfunctioning equipment or why Josie’s PCR experiment didn’t work. Add in teaching and administrative duties, and it’s a wonder that any science gets conducted at universities at all.

I consider this project still in progress- I will look into how much it will cost to get the equipment needed to do the work I have in mind and buy it out of my own pocket, and fly back to LA to do the work myself, if this is what’s needed.

What role does your gut microbiome (the sum of bacterial species living in your gut) play in your body’s immune response to vaccines? I address this question here:

I don’t go into a lot of detail, but it’s clear that the gut microbiome plays a role, and if I had to speculate about rare, adverse events, I’d speculate that they may be caused in part by your body’s past responses/ current overload or under-stimulation by the specific species of bacteria in your gut. Other factors will play a role too- like genetics- but I really do think your gut microbiome will play a significant part.

Happy reading!

Hi! Yesterday I drafted a non-technical article for The Conversation (where I discuss the plant microbiome in this article) on the subject of links between your gut microbiome and responses to vaccines. The article should be published sometime in February- I will post a link to it here when it is finished.

Work on Project: Cancer-Fighting Gut Bacteria is ongoing. It goes slowly, but it’s going!

Hello readers: today’s article is about how your lungs and your gut seem to interact: changes in gut microflora can affect lung activity, and vice versa. It is entitled, “Changes in the Bacterial Microbiota in Gut, Blood, and Lungs Following Acute LPS Instillation into Mice Lungs”. LPS is short for lipopolysaccharide, which is a component of the surface of some bacteria.

Here they were looking at total bacterial counts in blood and in the cecum (a region of the gut), as well as the microbiome composition present in lung fluid, blood, and the cecum. They found that adding LPS (it’s not clear what species the LPS is from, or if it is from a mixture of species) changed total bacterial counts in the cecum as well as the blood, and that adding antibiotics could reduce the changes seen in blood.

This evidence supports prior work indicating that, bacteria may translocate from the gut to the blood (where perhaps they interact with lung tissue) and indicates that the lungs- much like the gut- contain a large and diverse population of bacteria. More work is needed to characterize this environment and determine relationships between lung bacteria and lung dysfunction. The link to gut bacteria is also interesting- could this be why there are websites recommending different foods for helping people with asthma? Studies are inconclusive, but that may be expected if people weren’t taking the starting gut community into account when designing studies intended to determine if diet changes help asthma. A link between diet, your gut microbes, your lung microbes, and your breathing suggests all kinds of new ways to help treat asthma, and possibly other lung problems as well.

Hello, readers! Today’s interesting paper, which outlines evidence supporting the hypothesis that the composition of the bacteria in your gut will influence your eating behaviour, comes from Alcock et al. and was published earlier this year. The article is entitled, “Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms” and is found here.

To summarize this article, it’s thought that there may be several ways in which the composition of your gut bacteria might affect eating behaviour, and by doing so, affect phenomena like metabolic disorders, heart disease, or cancer. Some key points are listed below:

1. There is a selective influence of diet on the composition of gut bacteria: different bacteria eat or thrive on different nutrients, so what you eat will affect the composition of bacteria in your gut.

2. Microbes can manipulate host behaviour: This section outlines some studies which indicate that food cravings and mood are associated with differences in gut microflora. For example: a study in which chocolate cravings are associated with a changed gut bacterial composition can be found here. Additional evidence indicating that negative mood, or psychological shifts (e.g. “gut-brain axis”- related changes) can be associated with particular gut bacterial composition is given in this section. This might make sense if feeling anxious or unhappy leads to eating certain foods.  The authors suggest that by changing host psychology, gut microbes affect eating patterns.

3. Microbes modulate host receptor expression: Might gut bacteria alter host eating preferences by changing taste receptors in the host, which would make food taste different?

4. Microbes can influence hosts through hormones and effects on weight: Microbes can produce compounds which are similar in structure to mammalian hormones- and by so doing, can directly affect mood and behaviour, and probably directly affect physiological changes as well. There are studies describing links between metabolic disorders such as obesity with changes in gut bacterial communities, and other studies linking probiotics with changes in weight and weight-related phenomena. 

Further work on links between gut bacteria and eating habits may help us figure out how to make it easier for people to choose and maintain a healthy diet.