All posts for the month March, 2015

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.