I have neglected to post very much lately because of (a) work responsibilities (b) illness, and (c) for the past three weeks I’ve been using my spare time and energy to put together an academic grant application which, if successful, will pay for a lot of sequencing. Without the grant the work will still move forward, only sequencing (and, results) will have to wait until I have been able to raise funds to pay for it. I’ve learned from last year that crowdfunding is only mildly successful unless you know a lot of people- I do not know a lot of people, so I’m not giving that another try. I would rather take out a bank loan.

In the course of writing the grant application I’ve had to nail down specifics about what will be done in the labs of my various collaborators, and when. It’s exciting work! Material transfer agreements have been signed between my university, UCLA, and Duke, and two separate small projects will be conducted which, if successful, will shed light on the issue of whether my ideas for helping chemotherapy patients have any merit. They also may shed light on some basic mechanisms by which gut bacteria and their hosts communicate, which is pretty exciting.

In a related note, I’ve spoken with a researcher at Johns Hopkins and he has given me a lead on some exciting new methods that will really help my project, if I can find a way to convince someone to perform the assay for me (I am afraid I do not have enough expertise- and I’ve been away from bench work for more than a year! So I can’t do this myself).

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 probiotics.org.

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!

A material transfer agreement was signed between the University of Guelph and UCLA a few weeks ago, and once materials are prepared at UCLA and shipped here, my local collaborator and I will be able to start some tests. We are going to test products of a Lactobacillus johnsonii strain that has activity against lymphoma to see if those products can, by themselves, affect tumour growth or gene expression in tumour cells. How much work we do depends on how much stuff we get from UCLA. I will be paying for the sequencing myself, out of my personal funds, and so that will also be a limiting factor (some samples may have to sit in the freezer until I can afford to sequence them).

I’m encouraged by the in silico work I’ve done with the data I already have, and while that could be published, data from these planned experiments will make the paper so much stronger- so publication of the data I have is going to wait pending these results.

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.

Hello readers! Just last month an interesting paper was published on links between the composition of bacteria in the guts of alcoholics seeking treatment, and psychological or physiological symptoms that are associated with relapse. The paper is by Leclercq et al. and comes from a variety of European labs, and is published in the Proceedings of the National Academy of Sciences of the USA (find it here).

Essentially, the authors found that some, but not all, alcohol-dependent subjects developed gut leakiness, which was associated with higher scores of depression, anxiety, and alcohol cravings after a short period (three weeks) of abstinence in a treatment program. These may be important indicators of the potential for relapse. Subjects with gut leakiness had an altered composition of the gut bacterial community, and the bacteria were differently active (this was measured by studying the metabolic compounds that were present in feces).

What does this mean? It means that in some people, changes in gut bacterial community composition (dysbiosis) can lead to physical and psychological changes that affect mood, and possibly behavior. In this particular study, dysbiosis in the guts of some alcoholics resulted in effects that might make it more difficult for them to stay away from alcohol.

It may be possible in future to help people with substance abuse problems manage these problems with changes in diet and exercise! In fact, there’s no reason why a person can’t try to help manage these problems now by eating a healthy diet, getting regular sleep, and getting regular exercise. Probiotics may, in future, assist with problems like these but at the moment no products have been tested for helping with behavioral problems like alcohol abuse.