Dr. Emma Allen-Vercoe

Dr. Emma Allen-Vercoe
Professor, Canada Research Chair
Department of Molecular and Cellular Biology
Phone number: 
53366 / 54478
SSC 3252
SSC 3204

I began my research career with undergraduate and graduate studies at the Central Veterinary Laboratories (now Veterinary Laboratories Agency) and the Centre for Applied and Microbiological Research (CAMR, now the Health Protection Agency), UK, under the direction of Prof. Martin Woodward. There, I studied the enteric pathogen Salmonella enterica serovar Enteritidis, and developed a sound appreciation of the many obstacles that a enteric pathogen must overcome in the gut in order to cause disease. I became fascinated by the huge arsenal of virulence factors required by enteric pathogens in order to survive and proliferate in the gut environment.

I spent a brief postdoctoral period at CAMR, learning to work with technically challenging pathogens such as Mycobacterium tuberculosis and Campylobacter jejuni, before I relocated to Canada in 2001 to start a postdoctoral position at the University of Calgary, under the joint direction of Drs. Rebekah DeVinney and Mike Surette. Here I worked on Enteropathogenic and Enterohemorrhagic E. coli (EPEC and EHEC), using cell and molecular biology techniques to probe the fascinating interactions of their type III secretion systems with host cells. 

I had always been interested in learning more about the normal microbial population inside the human gut, and in 2004 I was fortunate enough to win a Fellow-to-Faculty Transition award through the Canadian Association of Gastroenterology. This award allowed me to develop an independent research program aimed at the study of the normal human microbiota and its influence on human health and disease, a program that I brought with me to Guelph in December 2007.

Since I’ve been here, with thanks to my very talented staff and students I have built a world-class anaerobic microbiology facility and directed it both towards answering fundamental research questions, and to create translational opportunities to move the science into the clinic.  In 2013, I co-founded NuBiyota, a company whose mission is to develop “Microbial Ecosystem Therapeutics” to treat disorders that have gut microbial dysbiosis as a root cause.

My motto: "My microbes told me to do it"
My hobbies: Gardening, reading, reading about gardening

  • B.Sc. (Hons) Biochemistry, University of London
  • Ph.D. Molecular Biology, Open University in conjunction with CAMR, UK Post-doctoral fellow, University of Calgary

Research in my laboratory is focused on the study of the normal human gut microbiota, both in disease and in health. The research can be loosely divided into several main areas centered on fundamental questions in the field of microbial ecology of the gut: 


The microbial world inside the human gut, though not without an intrinsic 'ick' factor, is a fascinating place, brimming with diversity on an enormous scale, but yet very poorly understood. Whilst molecular signatures have shown that the microbiota community within the gut can contain many hundreds of bacterial species, only a small percentage of these species are understood in terms of their biology. The lack of knowledge in this area stems from the fact that, as yet, the conditions required to culture most of the bacterial species resident in the human gut are not understood. In my laboratory, we are developing new techniques to culture and study novel bacterial species from the gut in order to better understand how these species might contribute to the remarkable homeostasis of the microbiota community as a whole. Central to our research approach, we have developed a continuous culture system to model the bacterial communities within the distal gut, the most densely populated part of the human body in terms of microbes. Dubbed the Robogut, our model contributes to many of the projects within the lab. Click this link to download a recent piece featuring this work on CBC's Quirks and Quarks' radio show.

We collaborate closely with Dr. Cezar Khursigara within MCB, and with his group we are developing cutting-edge methods to image and characterize microbial interactions within the gut, with a particular emphasis on understanding the interplay of the normal human flora with introduced probiotic bacteria. 

We had an extensive collaboration with the Broad Institute in Cambridge, Massachusetts, whereby we have provided a significant number of the bacterial isolates requested for genome sequencing through the Human Microbiome Project. We remain working closely with elements of this project, including the production of microbiological standards for HMP sequencing projects.


We are interested in the metabolic output of the gut microbiota and how this changes in response to environmental stimuli. We are interested in the response of the gut microbiota to drugs, food additives, and host proteins. Together with the Aucoin lab, University of Waterloo, we are exploring proton NMR as a tool for shotgun metabolomics of microbial ecosystems to help us understand metabolic shifts in response to microbiota perturbation. We currently apply this approach to the study of several diseases, including IBD, regressive autism, and neonatal necrotizing enterocolitis (NEC). 

We are also interested in the role of the virobiome – the viral microbiome, in intestinal health. Viruses are the most numerous components of the human gut microbiome, but their role in ecosystem development and dynamics is not well studied. The Robogut system offers us the perfect opportunity to study the interaction of the virome with the cellular components of the gut microbial ecosystem.


In a healthy person, despite the constantly changing environment within the gut, the resident microbiota maintain a largely homeostatic balance that is unique to the host. It is becoming increasingly clear that when this balance is shifted, so-called dysbiosis, the consequences to the host can be highly detrimental. My lab studies several key diseases with connections to the gut microbiota: Recurrent (refractive) Clostridioides difficile infection (CDI), colorectal cancer, diabetes and NEC.

A large part of the research in our lab is focused on determining which species, or groups of species, of the gut microbiota can behave pathogenically towards the host, and how. We are also using the Robogut to study the contributions of environmental factors, such as drugs, hormones and dietary components, to microbiota dysbiosis. 

CDI is an infection of particular and growing concern in the hospital setting, causing pain and serious diarrhea in affected patients.  C.difficile usually infects patients who have recently had a course of antibiotics, stripping them of their normal gut microbiota and allowing space for the pathogen to flourish.  Ironically, the current treatment for CDI is a further course of antibiotics to target the C.difficile.  Unfortunately, C.difficile can be very difficult to eradicate in this way, and some patients end up with a recurrent C.difficile infection that they are unable to clear, leaving them with no option but to take long-term doses of expensive antibiotics.  Fecal transplants offer a potential solution to this infection, by restoring normal flora and displacing the pathogen; however these carry a fairly high degree of risk themselves due to the potential presence of unknown pathogens in donor stool, and as well the procedure is messy and unpleasant.  We are working to produce a defined multi-species therapeutic ecosystem – a synthetic stool treatment that we have dubbed "RePOOPulate" – to overcome the problems of fecal transplants, while still offering a potential cure for CDI.   This work is being carried out in conjunction with NuBiyota, to create what we hope is an emerging paradigm in medicine.

Click on this link to download a Medical Post article describing this work. 
Click on this link to view a CTV The National piece that describes the use of RePOOPulate to treat a severely ill CDI patient.

Colorectal cancer is one of the leading forms of cancer in the world. Recently, in collaboration with the BC Cancer Agency, our lab has helped to demonstrate the overabundance of a particular anaerobic species, Fusobacterium nucleatum, in colorectal cancer tumours. This fascinating finding has opened the door to further studies that are underway to try to characterize the role that this enigmatic species may have in disease. In addition to this, we hope that our therapeutic ecosystem approach may be useful for treatment of CRC through reduction of F. nucleatum loads.

Diabetes is a serious metabolic disease where the body has difficulty in regulating blood sugar levels.  There are 2 main forms: type-1 (T1D), resulting from the pancreas producing insufficient amounts of insulin; and type-2 (T2D), resulting from a lack of response to insulin by the body’s cells.  There is a growing amount of evidence that the gut microbiota plays a role in the development of both conditions.  In T1D, exposure to certain microbial species found in the gut may trigger an autoimmune response to the insulin-producing cells of the pancreas in susceptible individuals.  In T2D, damage to the gut microbiota may result in an ecosystem that is metabolically imbalanced, in turn affecting metabolism of the whole body.  Our lab is working in conjunction with the lab of Jayne Danska, Sick Kids, to try to understand how, and which, gut microbes contribute to diabetes.

NEC is a serious disease that is particularly prevalent in preterm babies and has high morbidity and mortality rates. While we know that NEC is a disease that is directly related to the gut microbiota, what we don't yet understand is how the microbiota triggers NEC in some infants but not others, even when the same sorts of microbes are present in the gut. We are working in collaboration with researchers at the University of Chicago to try to understand how functional changes in the gut microbiota from preterm babies, perhaps influenced by the medical interventions that premature infants require, might trigger disease.

Understanding the mouse microbiome

Mice are frequently used as models for human disease, yet the mouse microbiome is poorly understood and varies according to e.g. housing conditions and animal genotype.  We are working to model the mouse gut microbiome and its function, with the hope of standardizing the laboratory mouse gut microbiota to promote reproducibility in animal models.

  • *National Institutes of Health, (NIH)
  • *Ontario Ministry of Agriculture, Food and Rural Affairs, (OMAFRA) 
  • *Natural Sciences and Engineering Research Council (NSERC)
  • *The Juvenile Diabetes Research Institute (JDRF)
  • *Pulse Crops (Canada) Association
  • *The Canadian Cancer Research Institute
  • Crohn's and Colitis Canada, (CCC)
  • US Department of Defense Congressionally Directed Medical ResearchProgram (CDMRP)
  • Physician’s Services Incorporated (PSI)
  • The Southeastern Ontario Academic Medical Organization (SEAMO)
  • *Canadian Institutes of Health Research, (CIHR)
  • Canada Foundation for Innovation, (CFI) 
  • Ontario Ministry of Research and Innovation, (OMRI) 
  • Ontario Centres of Excellence (OCE)
  • The Autism Research Institute

Past and *Present

Publications (since 2015) 

  • Klurfeld, D., Davis, C., Karp, R., Allen-Vercoe, E., Chang, E., B. Chassaing, G. Fahey, B. Hamaker, H. Holscher, J. Lampe, A. Marette, E. Martens, S. O'Keefe, D. Rose, M. Saarela, B., Schneeman, J. Slavin, J. Sonnenburg, K. Swanson, G. Wu, C. Lynch (in press, 2018).  Considerations for Best Practices in Studies of Diet and the Intestinal Microbiome.   American Journal of Physiology: Endocrinology and Metabolism.
  • Liu, C., Gu, H., Wright, B., Allen-Vercoe, E., & Beiko, R. (in press, 2018).  Phylogenetic clustering of genes reveals shared evolutionary trajectories and putative gene functions.   Genome Biology and Evolution.
  • Guzman-Rodriguez, M., *McDonald, J., Hyde, R., Allen-Vercoe, E., Claud, E., Sheth, P. and Petrof, E(in press, 2018).  Using bioreactors to study the effects of drugs on the human microbiota.   Methods
  • *Yen, S., *Bolte, E., Aucoin, M., & Allen-Vercoe, E. (2018).  Metabonomic evaluation of fecal water preparation methods: the effects of ultracentrifugation.   Current Metabolomics, 6 (1), 57-63.
  • Bogiatzi, C., Gloor, G., Allen-Vercoe, E., Reid, G., Wong, R., Urquhart, BL, Dinculescu, V, Ruetz, KN, Velenosi, TJ, Pignanelli, M, Spence, JD (2018).  Metabolic products of the intestinal mirobiome and extremes of atherosclerosis.   Atherosclerosis, 273, 91-97.
  • Gloor, G., Wong, R., Allen-Vercoe, E., Dinculescu, V., Pignanelli, M., Bogiatzi C, Reid, G, Spence, JD (2018).  Data on the gut and saliva microbiota from a cohort of atherosclerosis patients determined by 16S rRNA gene sequencing.   Data in Brief, 19, 481-485.
  • Pignanelli, M., Just, C., Bogiatzi, C., Dinculescu, V., Gloor, G., Allen-Vercoe, E., Reid, G., Urquhart, BL, Ruetz, KN, Velenosi, TJ, Spence, JD (2018).  Mediterranean diet score: associations with metabolic products of the intestinal microbiome, carotid plaque burden, and renal function.   Nutrients, 16 (10), E779.
  • Watkins, C., Murphy, K., *Yen, S., Carafa, I., Dempsey, E.M., O’ Shea, C.-A., Allen-Vercoe, E., Ross, P.R., Stanton, C. (2017). The effects of therapeutic hypothermia on the gut microbiota and metabolome of infants with hypoxic-ischemic encephalopathy. Intl J Biochem & Cell Biol. (accepted – in press).
  • Garcia, C, Tebbji, F, *Daigneault, M, Liu, N-N, Koehler, J, Allen-Vercoe, E, and Sellam, A. (2017) The human gut microbial metabolome modulates fungal growth via TOR signaling pathway.  MSphere (accepted – in press).
  • Sessenwein, JL, Baker, CC, Pradhananga, S, Maitland ME, Petrof, EO, Allen-Vercoe, E, Noordhof, C, Reed, DE, Vanner, SJ and Lomax AE. (2017) Protease-mediated suppression of DRG neuron excitability by commensal bacteria.  J Neurosci 37 (48): 11758-11768.
  • Casasanta, MA, Yoo, CC, Smith, HB, Duncan, AJ, *Cochrane, K, Varano, AC, Allen-Vercoe, E, and Slade, DJ. (2017).  A chemical and biological toolbox for Type Vd secretion: characterization of the phospholipase A1 autotransporter FplA from Fusobacterium nucleatumJ Biol Chem (in press).
  • Costea, P., Ehrlich, D., Dore, J., Bork, P., Guarner, F., IHMS partners (including Allen-Vercoe, E.), (2017). Towards standards for human fecal sample processing in metagenomic studies. Nature Biotechnology, 35 (11):1069-1076.
  • Van Raay, T. and Allen-Vercoe, E. (2017) Microbial interactions and interventions in colorectal cancer. Microbiology Spectrum, 5(3).
  • Murall C.L., Abbate J.L., Puelma-Touzel M., Allen-Vercoe E., Alizon S. Froissart R., McCann K., (2017) Invasions of host-associated microbiome networks. Advances in Ecological Research, 57:201-281.
  • Moniz, K., Ropers, M.-H., Dudefoi, W., Allen-Vercoe E., Walker, V. (2017) Impact of food grade and nanoTiO2 particles on a human intestinal community Food and Chemical Toxicology, 106 (PtA):242-249.
  • Belik, J., Shifrin, Y., Bottiglieri, T., Pan, J., *Daigneault, M., Allen-Vercoe, E. (2017) Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice. Scientific Reports, 12 (7): 39854.
  • Martz, S.-L. E., He, S.-M., Noordhof, C., Hurlbut, D.J., Gloor, G., *Carlucci, C., Weese, J.S., Allen-Vercoe, E., Sun, J., Claud, E.C. and Petrof, E.O.  (2016) A human gut ecosystem protects against Clostridium difficile disease by targeting TcdA. J. Gastroenterology 52(4): 452-465.
  • Das P., Saulnier, E., *Carlucci, C., Allen-Vercoe, E., Shah, V, Walker, V.K. (2016) Interaction between a Broad-spectrum Antibiotic and Silver Nanoparticles in a Human Gut Ecosystem.  Journal of Nanomedicine and Nanotechnology in press.
  • *Carlucci C, Petrof EO, Allen-Vercoe E. (2016) Fecal Microbiota-based Therapeutics for Recurrent Clostridium difficile Infection, Ulcerative Colitis and Obesity. EBioMedicine. Nov;13:37-45.
  • *Cochrane, K., McGuire, A. M., Priest, M. E., Abouelleil, A., Cerqueira, G. C., Lo, R., Earl, A.M., Allen-Vercoe, E., (2016). Complete Genome Sequences and Analysis of the Fusobacterium nucleatum subspecies animalis 7-1 Bacteriophage ɸFunu1 and ɸFunu2. Anaerobe. Apr;38:125-9.
  • Wissenbach D.K., *Oliphant K., Rolle-Kampczyk U., *Yen S., Höke H., Baumann S., Haange S.B., Verdu E.F., Allen-Vercoe E., von Bergen M.  (2016) Optimization of metabolomics of defined in vitro gut microbial ecosystems.  Int J Med Microbiol. Aug;306(5):280-9.
  • Munoz S., Guzman-Rodriguez M., Sun J., Zhang Y.G., Noordhof C., He S.M., Allen-Vercoe E., Claud E.C., Petrof E.O. (2016) Rebooting the microbiome. Gut Microbes. Jul 3;7(4):353-363.
  • Chamoun, E., Mutch, D.M., Allen-Vercoe, E., Buchholz, A., Duncan, A. M., Spriet, L.L., Haines, J. and Ma, D.W.L. (2016) A review of the associations between single nucleotide polymorphisms in taste receptors, eating behaviours, and health. Critical Reviews in Food Science and Nutrition. In press.
  • Gupta, S., Allen-Vercoe, E., & Petrof, E. (2016). Fecal transplantation-in perspective. Therapeutic Advances in Gastroenterology. Mar;9(2):229-39.
  • Jumas-Bilak, E., Bouvet, P., Allen-Vercoe, E., Aujoulat, F., Lawson, P., Jean-Pierre, H and Marchandin, H. (2015). Rarimicrobium hominis gen. nov., sp. nov., the fifth genus in the phylum Synergistetes that includes human clinical isolates. International Journal of Systematic and Evolutionary Microbiology. Nov;65(11):3965-3970
  • Costa, M., Staempfli, H., Allen-Vercoe, E., & Weese, S. (2015). "Development of the Fecal Microbiota in Foals," Equine Veterinary Journal.
  • Frye, R.E., Slattery, J., MacFabe, D.F., Allen-Vercoe, E., Parker, W., Rodakis J., Adams J.B., Krajmalnik-Brown R., Bolte E., Kahler S., Jennings J., James J., Cerniglia C.E., Midtvedt T. (2015). Approaches to studying and manipulating the enteric microbiome to improve autism symptoms. Microbial Ecology in Health & Disease (26), 26878.
  • Santiago-Rodriguez, T. M., Ly, M., *Daigneault, M., *Brown, I. H., *McDonald, J. A., Bonilla, N., Allen-Vercoe, E., Pride, D., (2015). Chemostat culture systems support diverse bacteriophage communities from human feces. Microbiome 3:58.
  • Allen-Vercoe, E. and Petrof, E.O. (2015). Using bugs as drugs: microbial ecosystem therapeutics. Canadian Communicable Disease Report 41S (5), 3-6.
  • Martz, S. L., *McDonald, J. A., Sun, J., Zhang, Y., Gloor, G. B., Noordhof, C., He, S.-M., Gerbaba, T., Blennerhassett, M., Hurlbut, D.J., Allen-Vercoe, E., Claud, E., Petrof, E.O., (2015). Administration of defined microbiota is protective in a murine Salmonella infection model. Scientific Reports. Nov 4 (5), 16094.
  • Natividad, J., Pinto-Sanchez, M.I., Galipeau, H.J., Jury, J., Jordana, M., Reinisch W., Collins S.M., Bercik P., Surette M.G., Allen-Vercoe E., Verdu E.F. (2015). Ecobiotherapy Rich in Firmicutes Decreases Susceptibility to Colitis in a Humanized Gnotobiotic Mouse Model. Inflammatory Bowel Diseases, 21 (8), 1883-93.
  • Link to complete set of publications: https://www.ncbi.nlm.nih.gov/pubmed/?term=llen-vercoe

Availability of microbial strains

The lab is often asked for stocks of microbial strains that have been deposited to the HMP reference genome collection (and that are not available through BEI Resources), or that are otherwise available in our considerable library of gut and oral microbial isolates. We are very happy to help, although the work has increased in volume in recent years. Therefore, we now ask that our requestors contribute to the cost of the preparation and QC of outgoing strains. Our standard cost is CAD$150 per strain (or CAD$400 to 'for profit' enterprise), as well as the cost of shipping. Requestors are responsible for acquisition of any import permits, as required. Some strains may be subject to the execution of a Materials Transfer Agreement (MTA) between the University of Guelph and the requestor's institution. Please address any questions about strain availability/MTA execution to Dr. Allen-Vercoe (eav@uoguelph.ca). Please note that many strains within our collection are fastidious anaerobes and require specific conditions for culture. gDNA can be prepared on request. 

Some of the Allen-Vercoe lab, August 2018

Some of the Allen-Vercoe lab, August 2018

Some of the Allen-Vercoe lab, September 2017

Some of the Allen-Vercoe lab, September 2017

Allen-Vercoe Lab, Summer 2016

(Most of) the Allen-Vercoe Lab, Summer 2016

CBS BBQ, 2014

The Allen-Vercoe Lab, CBS BBQ, June 2014

Gutsy Walk June 2012

The Allen-Vercoe lab, Gutsy Walk for the CCFC, June 2012


Kathleen Schroeter

Dr. Kathleen Schroeter
Process and Production Manager, NuBiyota

Kathleen is working on various aspects of manufacture and quality control of microbial ecosystem therapeutics products.
Motto: "May the force be with you"
Hobbies: Sports, sports and more sports, reading, gaming, cooking, hiking, spending time with her dogs 


Rafael Peixoto

Dr. Rafael Peixoto
Research Scientist, NuBiyota

Rafael is working to understand the interactions between sIgA molecules and the gut microbiota, and how these interactions might shape gut microbial communities. 
Motto: "What is essential is invisible to the eyes" 
Hobbies: Soccer, meditation, and travel.

Dr. Christian Carlucci
Research Scientist, NuBiyota

Christian works on the development and characterization of human gut microbiome therapeutics.  
Motto: "People don't forget" 
Hobbies: Playing in a rock 'n' roll band 

Dr. Kyla Cochrane
Research Scientist, NuBiyota

Kyla is NuBiyota’s bioinformatics expert and lends her skills to the development of novel ecosystem therapeutics.

Motto: “Think twice, code once” 

Hobbies: Painting, travel and my cat, Jones.


The NuBiyota production team

Joseph Ciufo

Motto: Don't count the days, make the days count.

Hobbies: Reading, Gaming, Rock Climbing and Fantasy Football 



Alyssa Koch

Motto: Such is life…

Hobbies: animals, reading, gym, cooking


Craig Moore

Motto: "Never tell me the odds"

Hobbies: Star Wars, Reading, Board/Video games, and spending time at the cottage


Keith Sherriff

Hobbies: Ultimate Frisbee, golf, and cooking 

Motto: Don't Panic 


AJ Stirling

Motto: "Don't take life too seriously, no one gets out alive anyway."

Hobbies: Cooking, gaming, running,  and binge-watching Netflix shows.


Kaitlyn OliphantKaitlyn Oliphant
Ph.D. candidate

Kaitlyn is studying gut ecosystems derived from patients with IBD in the Roboguts. Her project aims to understand what drives the dysbiosis in such ecosystems, and how such imbalance may be mitigated through the use of, e.g. probiotics. She is particularly focusing on the role of Lachnospiraceae family bacteria in gut microbial ecosystem function. 
Motto: "When a flight is proceeding incredibly well, something was forgotten." 
Hobbies: Travel, baking, aviation 


Sandi Yen

Sandi Yen
Ph.D. candidate

Sandi, who is co-supervised by Dr. Marc Aucoin, Univ. of Waterloo, is using the Robogut to model metabolic changes in gut microbial ecosystems, in turn using NMR-based metabonomics. She is applying these techniques particularly to the study of microbial ecosystem therapeutics (attempting to answer the question, "what makes a healthy ecosystem healthy?"). Sandi is also working to understand how metabolic changes in the gut modulate pathogenesis in neonatal NEC. For this work, our main collaborators are the Claud lab at the University of Chicago: https://microbiome.uchicago.edu/directory/erika-claud
Motto: "it is more like a big ball of wibbily wobbly timey wimey...stuff" 
Hobbies: ultimate Frisbee, board games, sci-fi shows 

Caroline Ganobis

Caroline Ganobis
M.Sc. candidate, preparing to transfer from M.Sc. to Ph.D. Caroline is working on adapting the Robogut model system to the culture of the mouse microbiome, in order to study how the microbial ecosystem of mice susceptible to colorectal cancer is perturbed during disease.
Motto: “Just be nice”
Hobbies: experimenting with foods, lifting things to be able to experiment with foods, and befriending dogs


Simone Renwick
Ph.D. candidate
Simone is creating defined microbial ecosystems from fecal samples collected from children who went on to develop type-1 diabetes.  She will use these model ecosystems to study the metabolite profiles of these ecosystems under different perturbation stress, and, in conjunction with the Danska lab at Sick Kids [please insert link: http://www.sickkids.ca/Research/Danska-lab/] , to understand the role of these ecosystems in immune system activation. 
Motto: I can and I will. 
Hobbies: Reading, Hiking, Painting and Chess

Jacob Wilde
Ph.D. candidate

Jacob is working to understand how the human gut virobiome can contribute to microbial ecosystem dynamics and interactions.  His project is being carried out in collaboration with the Pride lab [please insert link: http://www.thepridelaboratory.org/home.html] at the University of California, San Diego.
Motto: "No crackers, Gromit! We've forgotten the crackers!"
Hobbies: Insect evolution, insect poems, insect neurology, viruses, rugby, hockey, rugby.


Avery Robinson
Ph.D. candidate (start date January 2019)

Avery will be working to understand how Fusobacterium nucleatum can invade host cells, and its potential role as a modulator of colorectal cancer.
Motto: “Get $*it done!”
Hobbies: Cooking, writing, working weekends.

Mbita Nakazwe

Bioinformatics M.Sc. candidate 

Mbita is applying bioinformatics approaches to the analysis of metabolites and 16S rRNA gene profiles of infants at risk for developing type 1 diabetes.

Motto: Every day it gets a little easier. But you have to do it every day. That's the hard part.

Hobbies: Dancing, baking, yoga, bingeing TV/movies


Michelle Daigneault

Michelle Daigneault
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 Ambrose

Chris Ambrose
Lab ManagerChris 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. 
cambrose@uoguelph.ca   x 58007


Greg Higgins
Co-op student

Greg is working to create a new microbial ecosystem standard for use in gut microbiome sequencing projects
Motto: “You miss 100% of the shots you don't take”
Hobbies: Hockey, squash and TV dramas 




Connor Gianetto-Hill

Connor Gianetto-Hill
Co-op student

Connor is working with the NuBiyota research team to develop ‘microbial ecosystem therapeutics’
Motto: "Adapt and overcome”
Hobbies: Netflix, reading, cooking, horror movies



Project Students


Danielle Rose

Danielle is assisting Caroline in culturing the mouse gut microbiome

Motto: "Hope for the best, prepare for the worst" 

Hobbies: cooking, writing, and playing board games (like Catan). 


Erin Shackleton

Erin is helping Sandi to assess antibiotic levels in the premature infant gut

Motto: “Omnis cellula e cellula” 

Hobbies: Travel, yoga, kayaking, hiking, cycling 


Jackie Strauss

Jackie Strauss

Congratulations to Jackie Strauss, Ph.D. September 2011! Jackie's project was focused on understanding the role of the anaerobic pathogen, Fusobacterium nucleatum, in the etiology of IBD. 






Julie McDonald

Julie McDonald

Congratulations to Julie McDonald, PhD. May 2013! Julie's project focused on developing the Roboguts as a model of the human distal gut microbial ecosystem. Her project also examined the role of gut microbial biofilms in the maintenance of homeostasis during stress.




Ian Brown

Ian Brown

Congratulations to Ian Brown, M.Sc. June 2014. Ian studied the human distal gut microbiota's response to different resistant starches  derived from novel lines of maize. 




Kathleen Schroeter

Kathleen Schroeter

Congratulations to Kathleen Schroeter, PhD August 2014! Kathleen studied the role of various microbiota groups in biofilm formation in the distal gut. 
Co-supervised by Dr. Cezar Khursigara. 




Erin BolteErin Bolte

Congratulations to Erin Bolte, MSc April 2015!
Erin investigated the metabolic output of whole gut microbial communities cultured from autism spectrum disorder patients in the Roboguts, and assessed the effect of these metabolites on gut colonocytes in vitro




Mike Toh

Mike Toh
Congratulations to Mike Toh, PhD December 2015!
Co-supervised by Dr. Terry Van Raay, MCB, Mike developed the zebrafish embryo model as an innovative system to study the effects of gut bacterial metabolites on development, including neurogenesis and behaviour.




Kyla Cochrane

Kyla Cochrane

Congratulations to Kyla Cochrane, PhD February 2016! Kyla investigated virulence factors of Fusobacterium nucleatum as well as attempted to understand infectious synergies of F. nucleatum with other gut microbial species.




Christian Carlucci

Christian Carlucci

Congratulations to Christian Carlucci, PhD March 2017! Christian used the Roboguts to model the RePOOPulate ecosystem and to define the microbial species within this ecosystem and others like it that promote ecosystem robustness and resilience, with a particular emphasis on understanding potential mechanisms of action against C.difficile infection.