The Allen-Vercoe Lab Graduate Students
One of the most common in vivo models used in gastrointestinal and gut microbiome studies is the murine model. Mice possess a physiology and anatomy similar to humans, are inexpensive, have high reproductive rates and a short life cycle. However, a similarity mice and humans do not share is their gut microbiome. Compared to humans, mice differ genetically, consume a different diet, and are exposed to various environmental factors different to those found in most human environments. Each of these aspects shape the murine gut microbiome. Therefore, it is not surprising that differing mouse lines, or identical mouse lines with different housing conditions will display differing gut microbiomes. Collectively, these variations contribute to poor reproducibility and inconclusive results when using mice in lab experiments. As well, even mouse models which attempt to control differences in the microbiota fail to represent the true complexity and diversity found within the murine gastrointestinal tract. If we are to continue using mouse models as a proxy for human disease, one way to improve them may be to include a standardized murine-derived microbiome. My project, in collaboration with the Navarre Lab at the University of Toronto, aims to characterize the mouse gut microbiota, and to develop an in vitro model of the mouse colon in the Robogut that will help to standardize mouse models, and perhaps allow us to better understand their relevance to human health.
Motto: “Just be nice”
Hobbies: experimenting with foods, lifting things to be able to experiment with foods, and befriending dogs
Type 1 Diabetes (T1D) is one of the most common chronic diseases affecting children and the numbers of children being diagnosed has doubled in recent decades. Evidence from animal studies demonstrate that T1D incidence is associated with shifts in the composition of the gut microbiome. However, researchers are unsure of what triggers these changes in children. The objective of my research at the Allen-Vercoe lab is to investigate the gut microbiomes of infants to try to better understand the progression of T1D. Through a collaboration with Dr. Jayne Danska at the Hospital for Sick Children, I obtained stool samples from infants at risk of developing the disease—some of whom were subsequently diagnosed with T1D. I grew the microbes in these stool samples in ‘Robogut’ chemostat models that were designed to mimic the conditions of the human gut. The microbes formed stable communities within the chemostat vessels that resembled the communities in the infants that donated samples. Studying which microbes were present and what they were doing will give clues about their potential role in the development of T1D.
Motto: “Life is better when you’re laughing :)”
Hobbies: Reading, Hiking, Painting and Chess
My research involves the viral inhabitants of the human gut. Most of the living things in our gut are bacteria, so it comes as no surprise that most gut viruses infect bacteria, and bacteria only. Sometimes these bacterial viruses kill the cells they infect, and sometimes they ‘upgrade’ them with genetic novelties. In the latter case, the virus usually ‘hides’ inside the host-bacterium, piggy-backing on the success of its recently upgraded bacterial vessel. In most bacterial ecosystems, such as those in fresh water or soil, piggy-backing viruses are the minority. In the human gut, they are the majority.
Currently, I am seeking to understand how communities of piggy-backing viruses are formed in our gut, how they are maintained, and how they influence the bacterial populations that call our bowels 'home.' In other words, I am asking, “How did they get there? What can they do? How important are they for the fitness and health of a human?” I am doing this in collaboration with the Pride lab at UC San Diego.
To us, viruses are agents of disease. While many animal viruses are certainly to blame for a large portion of human suffering, many others are friendly to us. In fact, 7% of the human genome is composed of piggy-backing animal viruses that—like their bacteria-infecting counterparts—‘hid’ inside our ancestors’ cells many thousands of years ago. These invaders have been hiding inside our cells for so long, they’ve forgotten how to get themselves out again! They are now permanent fixtures of our genetic code – the stuff that makes us ‘us.’ The same invasions are currently happening to the bacteria in our guts, but on a much faster and more dynamic scale. These invaders are abundant, adaptive, and unknown. If we are to truly understand what it means for a gastrointestinal ecosystem to be ‘healthy,’ we must first understand how these viruses influence the lives of their bacterial hosts.
Motto: "No crackers, Gromit! We've forgotten the crackers!"
Hobbies: Insect evolution, insect poems, insect neurology, viruses, rugby, hockey, rugby.
Fusobacterium nucleatum (Fn) is a common bacterial member of the human oral
microbiome—and it is an opportunist. When Fn is found elsewhere in the human body, the microbe is typically associated with disease, and colorectal cancer (CRC) is one such disease. In fact, the presence of Fn in the tissues can often predict a poor outcome. Unfortunately, we don’t know much about how Fn causes disease, and whether all of the other microbes present in the colon, the colonic ‘microbiota’ influence this process.
To make a start in understanding disease processes, scientists often use animal or tissue culture models such as mice and ‘organoids’ (small pieces of tissue), respectively. In the case of mice, we don’t yet understand whether Fn affects these animals in the same way it does humans. To address this, the first part of my research is aimed at understanding how well the mouse model of Fn disease matches what happens in human disease, at a molecular level. To do this, I will use cultured mouse cells and the equivalent human cells and infect them with Fn, then track the effects of infection at a molecular level using microscopy, to visualize the cells, and a technique called ‘RNA-seq’, which allows us to see how the cells are behaving.
The next part of my project is to understand how Fn might be influenced in its ability to cause disease by determining whether the colonic microbiota plays a role in infection. Members of the microbiota may be neutral bystanders to the process of Fn infection, but alternatively they may influence Fn by either helping or hindering the pathogenic process. I will carry out infection experiments in the presence of absence of selected microbes from the colon, and from this I should be able to see if there are certain microbes that, when present, may alter the course of Fn mediated disease.
Finally, since it is known that microbes communicate with each other using a chemical language, I am interested to find out whether Fn can respond to the language of the gut microbiota alone, and whether this is enough to alter the cause of infection. I will culture whole microbial ecosystems from the colons of both diseased and healthy people using a customized apparatus called a ‘Robogut’. The Robogut mimics the human colonic environment, allowing us to grow most of the microbes present in a human colon, using, for example, poop as a starting point. Once the ecosystems are growing well, I will harvest some of this material and extract the molecules from the sample, without the microbes, and use this to see whether Fn can respond to this chemical language alone. If it does, there is great value in understanding which molecules Fn responds to in particular. This, and the outcomes of my other work will help in the development of novel therapies, diagnostic techniques or prevention strategies for CRC.
Motto: “Get $*it done!”
Hobbies: Cooking, writing, working weekends.
Bdellovibrio-and-Like Organisms (BALOs) are bacteria that have a unique lifestyle; they are predatory bacteria that attack and kill other bacterial species. The majority of the BALOs do this by squeezing inside the prey bacteria and using enzymes to dissolve the contents of the bacterial cell for use as food. One they have eaten their prey, the BALOs multiply and then pop out of the digested prey cell to continue their lifecycle on further prey. BALOs do not predate all bacterial cells, but only those with a double membrane – ‘Gram negative’ species.
There are several bacterial species that are known to play a role in the pathogenesis of colorectal cancer (CRC). These are certain forms of E. coli, Bacteroides fragilis, and Fusobacterium nucleatum, collectively known as ‘oncomicrobes’. All of these species are Gram negative, and thus potentially vulnerable to attack by BALOs. Instead of treating a patient with broad-spectrum antibiotics, which risks promoting antibiotic resistance and damaging the microbial environment of the colon, could predatory bacteria be put to work to remove undesirable, cancer-promoting microbes from the colon?
The current goal of my research is thus to isolate BALOs from the environment and to then test them for their predation efficacy against oncomicrobes such as F. nucleatum. Those that are shown to be efficient predators will be further ‘trained’ to improve their predatory behaviour within conditions such as those found within the human gut (37°C and no oxygen). The hope is to find BALO strains which are effective predators against CRC-promoting oncomicrobes, and could be used therapeutically to reduce or remove such oncomicrobes from the colon without damaging the rest of the microbiota or the colon itself.
Motto: “Life moves pretty fast. If you don't stop and look around once in a while, you could miss it.”
Hobbies: Hockey, Squash, Skiing, Travelling, TV/Movie Thrillers
M.Sc. candidate (co-supervised with Dr. Josephy)
The food we eat can directly impact our health, so it is important to understand what we are ingesting in our day-to-day life. Many food products are coloured using dyes to improve the presentation of food. Synthetic food dyes are used more commonly used than natural dyes because they are cheaper to produce and typically last longer. Azo dyes are a type of synthetic dye that can have very vibrant colours and be produced easily so they are used in lots of food products that are consumed around the world. Azo dyes have a specific bond that is broken down, or metabolized, by enzymes called ‘azoreductases’. Azoreductase enzymes are present in our gut bacteria, meaning that these dyes will be broken down into new products within our digestive tract. Azo dyes were first synthesized for commercial use around the beginning of the 19th century. However, after these dyes had been approved for use in commercial food products it was found that when the azo dyes are metabolized some products formed are carcinogenic. The United States, European Union and Canadian and governments decided to ban many azo dyes from use in food products after several researchers found that there was a link between these dyes and cancer.
Today there are still four azo dyes that are allowed in Canada to be used in food; Amaranth, Sunset Yellow, Allura Red and Tartrazine. More recently consumers have been boycotting foods with azo dyes. My research is focused on the dye Tartrazine since there seem to be many sensitivities to this dye and may be linked to hyperactivity in children. Children are the most susceptible to ingesting high amounts of azo dyes since many of foods targeted to children are brightly coloured, making it is easier for them to reach the acceptable daily intake (ADI). The ADI is set in place because ingesting high doses of dye can have adverse consequences.
My research is looking at the metabolites formed by these dyes within the gut. I am using bacterial strains found in the healthy human gut and determining which strains can metabolize azo dyes. Once I have determined the bacterial strains that can metabolize the dyes, my goal is to analyze what products are being created and looking at their molecular structures to determine their effects on our intestinal cells. I hope to further the understanding of azo dye metabolism by our gut bacteria and how these metabolites could affect human health.
Motto: "If you always keep both feet planted firmly on the ground, you'll have trouble putting your pants on"
Hobbies: hiking, swimming, playing guitar, and hanging out with dogs
It has been shown that the gut microbiomes of western populations have over time become less diverse than that of our ancestors and traditional hunter-gatherer groups that remain isolated, such as the Yanomami in Venezuela, or the Tunapuco in Peru. The ‘missing microbe hypothesis’ postulates that this loss in microbiota is influencing the rise of diseases such as diabetes, obesity, and inflammatory bowel disease, which are rarely seen in traditional populations. My project will use the Robogut system to model traditional gut ecosystems to culture and isolate as many species as possible, using stool samples obtained from traditional groups to seed it. The microbes that are not commonly found in the gut microbiome profiles of western populations can then be characterized to determine their biological importance. This project will also determine if these missing microbes could provide additional functionality to the western gut, which could be used in potential therapeutics to address conditions caused by gut microbiome dysbiosis. These questions can be investigated by studying the community dynamics, such as metabolic output, of western-like gut communities on the Robogut platform that are supplemented with microbes of interest. The results of this project will help us better understand the historic role of the human gut microbiome, and if re-introducing lost species could improve the functionality of the gut microbiome of westernized populations.
Motto: "Just keep swimming!"
Hobbies: "Reading, re-watching The Office or Doctor Who, knitting"
M.Sc., Research Tech.
Michelle contributes her considerable technical expertise to all of the projects within the lab, and also oversees the work to culture, characterize and archive novel bacterial species from the human gut. If you don't know how to culture a microbe, ask Michelle, as she probably does!
Motto: "Hakuna matata"
Hobbies: Volleyball, addictive TV shows, more volleyball ...
Chris does all the things that keep the lab running smoothly, including animal work, biosafety, purchasing and accounting, shipping and receiving paperwork, due diligence and maintenance & repair of equipment. He also is the go-to person for batch and chemostat fermentation method development.
Motto: "If you're not going to do it right, don't bother!"
Hobbies: Watching bad reality TV shows, wind-gazing, fixing stuff.
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