The Editorial Office of Microbiome Research Reports (MRR) was pleased to have a special interview with Prof. Emma Allen-Vercoe, Executive Editor of the journal, on January 9, 2023.
About Prof. Emma Allen-Vercoe
Prof. Allen-Vercoe is the recipient of several awards for innovation and outreach and is currently the Canada Research Chair in Human Gut Microbiome Function and Host Interactions. Prof. Allen-Vercoe's research focuses on the microbial ecology of the human gut, and she runs one of the few laboratories in the world equipped to culture the often highly fastidious and anaerobic microbes found in the human gut, both axenically and as part of defined, complex communities (using bioreactor technology). She is a contributor of many isolates to the Human Microbiome Project strain collection, and she participates in several ongoing efforts to standardize the measurement of the microbiome.
About her High-Cited Article in MRR, "Deteriorating microbiomes in agriculture - the unintended effects of pesticides on microbial life":
1. This review was supported by Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant (RGPIN-2020-05647) and NSERC Postdoctoral Fellowship Award (PDF-558010-2021).
2. This review outlined the multifaceted ways in which agricultural chemicals can disrupt microbial ecosystem function using examples from honey bees and crop plants. There is a pressing need to reassess the use of agrochemical xenobiotics through the lens of microbial ecology and the concurrent or subsequent effects on host (animal and plant) physiology.
Focus Interview Questions:1. Firstly, congratulations on your excellent contribution "Deteriorating microbiomes in agriculture - the unintended effects of pesticides on microbial life" for it ranks now as the most cited article in MRR. What do you think makes this review article a success?
Thank you. I am excited that this work has received so much interest. I have to credit my postdoctoral associate, Dr. Brendan Daisley, for his hard work and vision in the writing of this paper with me. Brendan joined my lab almost 18 months ago to work on the insect microbiome using some of the methods we have developed in the lab to study the mammalian microbiome. It is Brendan, whom I credit for getting me excited about insect microbiomes; there is so much untapped potential and it is becoming increasingly important to understand the microbial world around us. I now appreciate that insect microbiomes are just as important to study as the human microbiome! I think one aspect that makes our recent review article a success is that it attempts – and I think it succeeds – to pull together a rationale for why it is so important to determine how anthropogenic activities disrupt the insect world around us. Pointing to the gaps in scientific research and government policies in this area (and there are many gaps) is the first step in bringing this to the attention of scientists, who we hope will be able to collectively develop ways to tackle the problems.
2. I noticed that your motto is "My microbes told me to do it". What are the implications of this motto?
It's really a bit of whimsy. When I started my lab, this was around the time that research had begun to illuminate the role that the mammalian gut microbiome plays in the gut-brain axis and the influence it has on behaviour. My colleagues, lab members and I would often discuss the implications of this, and that maybe we humans were automatons controlled by the microbes living inside of us! I joked that this would make us humans mostly blameless for our actions, and the motto was born!
3. What projects are you currently working on?
I’m working on many different projects at the moment, probably too many, but all of them interest me greatly, so it’s hard to curb any of them!
A major direction in my lab is the study of so-called VANISH (Volatile and Negatively Associated with Industrial Societies of Humans) microbes. These are microbes that can be seen associated with societies that have had little or no modern lifestyle interventions (for example, no or few antibiotics, limited but high fibre diets, etc.). It turns out that there are a few bacterial species, for example, that can be found in hunter-gatherer societies around the globe, but which only very rarely, or never, are found in industrial societies. We've been working to culture some of the gut microbiome representatives of these VANISH taxa, and characterize them so that we can understand whether their loss from the industrial microbiome has been compensated for by the gain of other taxa, and/or whether there is a consequent deficit in microbiome function associated with missing microbes.
Another major project in the lab is the study of fusobacteria, a group of anaerobic species which seem to have some emergent pathogenic properties. We've studied this microbe for a long time, but we have more recently become interested in the connection between this microbe and the development and perpetuation of both oral and colorectal cancer. So we have a number of projects looking variously at how fusobacteria (and particularly F. nucleatum) interacts with other microbes from the microbiome, and with the host, in this context, and how this is affected by diet.
Keeping in with the theme of diet, my lab has a long-standing collaboration with the lab of Jayne Danska at Toronto's Hospital for Sick Children; here, we are working to define gut microbial signals that initiate or perpetuate immune dysfunction (in Type 1 diabetes) or insulin resistance and obesity (in type 2 diabetes). We've also become very interested in how human milk oligosaccharides influence gut microbial behaviour and perhaps offer some protection in the context of T1D development.
My lab has been interested in bacteriophages for some time, and we are using our bioreactor system that models the human colonic microbiome to try to define the roles of temperate bacteriophages in microbial ecosystem dynamics.
And finally, as mentioned, the insect gut microbiome is becoming a current major direction for the lab, focusing on the honey bee gut microbiome. We have started to develop methods to culture the honey bee gut microbiome in bioreactor systems in vitro, which allow us to further try to understand the functional attributes of the microbes in bee health, as well as to determine how commonly used agrochemicals affect microbial ecosystem biology. This is an exciting new area for the lab, and we recently launched the Canadian Bee Gut Project as a way to monitor honey bee gut microbiome composition across the country, and correlate this to major stressors in the industry, including overwintering survival, climate change and exposure to common pesticides and herbicides.
As well as my academic lab, I am also the CEO of a company that I co-founded almost 10 years ago (NuBiyota) to develop novel microbial therapeutics from live bacteria isolated from the guts of supremely healthy individuals. Thus, there are also research activities in this area, which keep me busy and focused on the incredible potential of gut-associated bacteria!
4. How do you balance your time? What is your typical day like?
A typical day starts with an early morning and a workout, either swimming, weights or cardio, to try to keep fit, but also workout time for me is thinking time; I have some of my best research ideas in the pool! At my office, I usually balance my time between teaching and meeting with my graduate students. It's becoming more and more difficult, but I try to schedule meetings to leave at least one afternoon free per week for writing. I am currently teaching a lab-based course, so I lecture once a week to undergraduates, but also pop into the lab sessions to interact with the students. Like most academic researchers, I always seem to have a grant application on the go, and so I try to put time aside each week to work on aspects of these, as well as manuscripts and NuBiyota research planning. Recently I crystallized a new group of microbiome researchers at my university, and so I'm also currently organizing the inaugural meeting for this. For the sake of my family, I try hard to finish work by 6 p.m. each day and have dinner with my husband and my younger daughter (I often help her with her high school biology homework afterwards!). My elder daughter has moved abroad and so I catch up with her on the weekends.
5. Describe a research problem you have faced. What did you learn from it?
One of the biggest research 'problems' that I (and many contemporary life science researchers) face is that it is becoming increasingly difficult to carry out scientific research projects in isolation. What I mean by that is that the interconnectedness of many different systems in biology is becoming more and more apparent, and so it often becomes necessary to study a research question from many angles in order to make sense of it. For example, it becomes difficult to study just the microbiology of the human gut microbiome in isolation of the fields of ecology, gastroenterology, infectious disease, bioinformatics, immunology, chemistry… and many others. Why is that a problem? Well, it is not possible to be an expert in dozens of rapidly moving fields. Therefore, something I learned early in my career is that there is great power in meaningful collaboration. I try to resist the temptation to be overly competitive, even though research funding is becoming harder and harder to obtain; I hope that this will eventually improve. It is important to me that scientists make progress in research as a collective; there are more than enough important research questions to go around.
6. Why are you now studying the insect microbiome? What do you hope to achieve?
As I mentioned, my postdoctoral associate, Dr. Daisley, introduced me to the world of insect microbiomes, and it didn't take long for me to become deeply fascinated. We are specifically looking at the microbiome health of honey bees, which, as I think most people realize, are critical pollinator species that directly influence agricultural practices and success. Honey bee microbiomes, like many human microbiomes, are in decline. There are parallels to why and how this may be happening for both humans and honey bees, and so it has not been as much of a stretch as it sounds to apply my lab's expertise to this additional research area. As honey bees are social insects, there are also many questions to answer about how their microbiomes influence the production of pheromones and their subsequent behaviour. What we hope to achieve is a better understanding of how microbiomes influence insect biology, and how we can help to remediate diminishing microbiomes to improve insect health. While we focus on honey bees, we expect our investigations to be equally relevant to native insect pollinator species, which remain understudied.
Respectfully Submitted by the Editorial Office
Microbiome Research Reports