Dr. Emma Allen-Vercoe

Dr. Emma Allen-Vercoe
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.

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 have an extensive collaboration with the Broad Institute in Cambridge, Massachusetts, whereby we have provided, and continue to provide, a significant number of the bacterial isolates requested for genome sequencing through the Human Microbiome Project


We are interested in the metabolic output of the gut microbiota and how this changes in response to environmental stimuli. We are involved in an ongoing project in collaboration with Agriculture and Agri-Food Canada to determine how the colonic microbiota derived from different individuals responds to dietary substrates derived from pulses that are processed in different ways, with a view to understanding how diet may be tailored to microbiota types to enhance health. We are also 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 most recently, neonatal necrotizing enterocolitis (NEC). 


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: IBD, regressive (late-onset) autism, recurrent (refractive) Clostridioides difficile infection (CDI), colorectal cancer, diabetes and NEC.

IBD is an umbrella term for two debilitating diseases; Crohn's Disease (CD) and Ulcerative Colitis (UC). These diseases are characterized by the formation of gut lesions that are somehow triggered by dysbiosis of the microbiota. 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. 

Regressive autism is a form of autism spectrum disorder that is characterized by apparently normal development in infancy followed by a sudden regression of social and behavioural skills, usually between 24-36 months of age. In most cases, disturbances and inflammation in the gut are also seen, and several studies have shown an apparent dysbiosis within the gut microbiota of these patients, with certain bacteria belonging to select groups of bacteria predominating. We are working to try to further characterize the microbiota of autistic patients, and to determine whether certain bacterial products may somehow be involved in the etiology of this distressing condition. This work is carried out in conjunction with our collaborators at the Kilee Patchell-Evans Autism Research Group at the University of Western Ontario, led by Dr. Derrick MacFabe. 

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 probiotic – a synthetic stool treatment that we call "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 our clinical collaborators at Queen’s University/Kingston General Hospital.  Recently, Dr. Allen-Vercoe co-founded a spin-off company, Nubiyota, to help pursue “Microbial Ecosystem Therapeutics” as an emerging new 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.  

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.

The gut microbiota of livestock animals
The lab's work has so far been focused on the human gut microbiota (the collection of microbes in the gut), and its importance to our wellbeing. However, a long, hard look at the methods through which animals are intensively reared for food production has led Dr. A-V to start to consider how modern interventions in animal husbandry might damage the gut microbes, and hence the health, of farm animals. What is clear, for both humans and animals, is that modern living has eroded the microbial diversity of the gut, and this lack of diversity may underlie a whole range of different diseases. We are turning our attention to the gut microbiota of pigs as our first foray into veterinary microbiota research. In pigs, a lack of gut microbiota diversity may contribute to infection, failure to thrive, and other health problems that currently plague pork producers. 

What if we could replace the missing microbes and by doing so, restore health to farmed animals? We are working to create a healthy gut microbial ecosystem for pigs - kind of like a 'super-probiotic' that contains the microbes that intensively reared animals might be missing. For this project we are working with the de Martines family of Perth Pork Products, near Stratford Ontario, who raise a herd of wild boar in a close-to-natural setting; understanding the diversity contained within these animal guts is a first step to understanding how we might be able to improve gut health in intensively reared animals.  

  • *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

  • 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 in press.
  • 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, in press.
  • 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, in press.
  • Yen, S., Bolte, E., Aucoin, M. and Allen-Vercoe, E. (2017) Metabolomic evaluation of fecal water preparation methods: the effects of ultracentrifugation. Current Metabolomics, 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.
  • Martz, S., He, S., Noordhof, C., Hurlbut, D. J., Gloor, G. B., Carlucci, C., Weese, J.S., Allen-Vercoe, E. Sun, J., Claud, E.C. Petrof, E.O. 2016.  A human gut ecosystem protects against C. difficile disease by targeting TcdA.   Journal of Gastroenterology (in press). 
  • Munoz S, Guzman-Rodriguez M, Sun J, Zhang YG, Noordhof C, He SM, Allen-Vercoe E, Claud EC, Petrof EO.  Rebooting the microbiome. Gut Microbes. 2016 13:1-11.
  • Wissenbach DK, Oliphant K, Rolle-Kampczyk U, Yen S, Höke H, Baumann S, Haange SB, Verdu EF, Allen-Vercoe E, von Bergen M.  Optimization of metabolomics of defined in vitro gut microbial ecosystems. Int J Med Microbiol. 2016 (in press).
  • Gupta, S., Allen-Vercoe, E., & Petrof, E. Fecal transplantation-in perspective.Therapeutic Advances in Gastroenterology 2015 9L229-39. 
  • Allen-Vercoe, E. & Petrof, E.O. Using bugs as drugs: Microbial ecosystem therapeutics. Canada Communicable Disease Report 2015 (in press).
  • Santiago-Rodriguez, T. M., Ly, M., Daigneault, M., Brown, I. H., McDonald, J. A., Bonilla, N., Allen-Vercoe, E., Pride, D., (2015). Human fecal cultures support diverse phage communities. Microbiome 2015 (in press). 
  • Cochrane K, McGuire AM, Priest ME, Abouelleil A, Cerqueira GC, Lo R, Earl AM, Allen-Vercoe E. Complete Genome Sequences and Analysis of the Fusobacterium nucleatum subspecies animalis 7-1 Bacteriophage φ Funu1 and φ Funu2.  Anaerobe. 2016 38:125-9.
  • Martz SL, McDonald JA, Sun J, Zhang YG, Gloor GB, Noordhof C, He SM, Gerbaba TK, Blennerhassett M, Hurlbut DJ, Allen-Vercoe E, Claud EC, Petrof EO. Administration of defined microbiota is protective in a murine Salmonella infection model. Sci Rep. 2015 5:16094. doi: 10.1038/srep16094. 
  • Costa MC, Stämpfli HR, Allen-Vercoe E, Weese JS. Development of the faecal microbiota in foals. Equine Vet J. 2015 (in press)
  • Jumas-Bilak E, Bouvet P, Allen-Vercoe E, Aujoulat F, Lawson PA, Jean-Pierre H, Marchandin H. Rarimicrobium hominis gen. nov., sp. nov., the fifth genus in the phylum Synergistetes that includes human clinical isolates. Int J Syst Evol Microbiol. 2015 (in press) 
  • Natividad JM, Pinto-Sanchez MI, Galipeau HJ, Jury J, Jordana M, Reinisch W, Collins SM, Bercik P, Surette MG, Allen-Vercoe E, Verdu EF. Ecobiotherapy Rich in Firmicutes Decreases Susceptibility to Colitis in a Humanized Gnotobiotic Mouse Model. Inflamm Bowel Dis. 2015 8:1883-93. 
  • Frye RE, Slattery J, MacFabe DF, Allen-Vercoe E, Parker W, Rodakis J, Adams JB, Krajmalnik-Brown R, Bolte E, Kahler S, Jennings J, James J, Cerniglia CE, Midtvedt T. Approaches to studying and manipulating the enteric microbiome to improve autism symptoms. Microb Ecol Health Dis. 2015 26:26878. 
  • Yen S, McDonald JA, Schroeter K, Oliphant K, Sokolenko S, Blondeel EJ, Allen-Vercoe E, Aucoin MG. Metabolomic analysis of human fecal microbiota: a comparison of feces-derived communities and defined mixed communities. J Proteome Res. 2015 14(3):1472-82. 
  • Das, P., McDonald, J., Petrof, E., Allen-Vercoe, E., & Walker, V. Nanosilver-mediated change in human intestinal microbiota. Journal of Nanomedicine & Nanotechnology. 2014 5:5.  
  • Costa, M., Stämpfli, H., Arroyo, L., Allen-Vercoe, E., Gomes, R., Weese, J.S. Changes in the Equine Fecal Microbiota Associated with the Use of Systemic Antimicrobial Drugs.  BMC Veterinary Research. 2015 11:19.
  • Allen-Vercoe, E. & Toh, M.   The Human Gut Microbiota with reference to Autism Spectrum Disorder: considering the whole as more than a sum of its parts.  Microbial Ecology in Health & Disease. 2015 Jan; 26:26309.
  • McDonald JA, Fuentes S, Schroeter K, Heikamp-deJong I, Khursigara CM, de Vos WM, Allen-Vercoe E.  Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model.  Microbiol Methods. 2015 Jan;108:36-44.
  • Allen-Vercoe E.  Fusobacterium varium in Ulcerative Colitis: Is It Population-Based? Dig Dis Sci. 2015 Jan; 60(1):7-8.
  • Manson McGuire A, Cochrane K, Griggs AD, Haas BJ, Abeel T, Zeng Q, Nice JB, MacDonald H, Birren BW, Berger BW, Allen-Vercoe E, Earl AM.  Evolution of invasion in a diverse set of Fusobacterium species. MBio. 2014 Nov 4;5(6):e01864.
  • Allen-Vercoe, E. & Jobin, C. Fusobacterium and Enterobacteriaceae: important players for CRC? Immunology Letters Dec;162(2PA):54-61.
  • Antunes, C. M., McDonald, J. A., Schroeter, K., Carlucci, C., Ferreira, R. B., Wang, M., Yurist-Doutsch, S., Hira, G., Jacobson, K., Davies, J.E., Allen-Vercoe, E., Finlay, B.B.  Anti-virulence activity of the human gut metabolome.   mBio. 2014 Jul 29;5(4):e01183-14.
  • Correa-Betanzo, J., Allen-Vercoe, E., McDonald, J. A., Schroeter, K., Corredig, M., Paliyath, G. Stability and biological activity of wild blueberry (Vaccinium angustifolium) polyphenols during simulated in vitro gastrointestinal digestion.   Food Chemistry.  2014 Dec 15;165:522-31.
  • Brace, C., Gloor, G, Ropeleski, M., Allen-Vercoe, E., Petrof, E.  Microbial composition analysis of Clostridium difficile infections in an ulcerative colitis patient treated with multiple fecal microbiota transplantations. Journal of Crohn’s and Colitis.  2014 pii: S1873-9946(14)00039-7.
  • Allen-Vercoe, E. and Petrof, E.  The microbiome: what it means for medicine.  British Journal of General Practice. 2014 Mar;64(620):118-9.
  • McDonald, JA, Schroeter, K, Fuentes S, Heikamp-Dejong, I, Khursigara, CM, de Vos, WM, Allen-Vercoe, E.  Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model.  J Microbiol Methods. 2013 95(2):167-174.
  • Allen-Vercoe, E.  Bringing the gut microbiota into focus through microbial culture: recent progress and future perspective. Curr Opin Microbiol. 2013 16(5):625-9.
  • Allen-Vercoe, E. and Petrof, E.O. Artificial stool transplantation: progress towards a safer, more effective and acceptable alternative. Expert Review of Gastroenterology & Hepatology. 2013 May;7(4):291-3.
  • Warren RL, Freeman DJ, Pleasance S, Watson P, Moore RA, Cochrane K, Allen-Vercoe E and Holt RA.  Co-occurrence of anaerobic bacteria in colorectal carcinomas.  Microbiome. 2013 May 1:16.
  • Pequegnat B, Sagermann M, Valliani M, Toh M, Chow H, Allen-Vercoe E, Monteiro MA. A vaccine and diagnostic target for Clostridium bolteae, an autism-associated bacterium. Vaccine. 2013 Jun 10;31(26):2787-90.  
  • Toh, M., Allen-Vercoe, E., Daigneault M., Goodyear, M., Van Raay, T. Colonizing the embryonic zebrafish gut with anaerobic bacteria derived from the human gastrointestinal tract.  Zebrafish. 2013 Jun;10(2):194-8.
  • Petrof, E.O., Gloor,G.B., Vanner,S.J., Weese,S.J. Carter, D., Daigneault, M.C.,  Brown, E.M., Schroeter, K. and Allen-Vercoe, E. Synthetic stool transplant therapy for the eradication of Clostridium difficile infection: "RePOOPulating" the gut.  Microbiome1:3 (9 January 2013, highly accessed).
  • Petrof, E.O, Claud, E.C., Gloor, G.B. and Allen-Vercoe, E.  Microbial Ecosystems Therapeutics – a New Paradigm in Medicine?  Beneficial Microbes, 2013 Mar 1;4(1):53-65.
  • Shahinas, D., Silverman, M., Sittler, T., Chiu, C., Kim, P., Allen-Vercoe, E., Weese, J.S., Wong, A., Low D.E., Pillai, D.R. Changes in microbial diversity associated with fecal transplantation based on 16S deep sequencing. MBio. 2012 Oct 23;3(5).
  • Allen-Vercoe, E., Daigneault, M., White, A.P., Panaccione, R., Duncan, S., Flint, H., O’Neal, L. and Lawson, P. Anaerostipes hadrus comb. nov., a dominant species within the human colonic microbiota; reclassification of Eubacterium hadrum Moore et al. 1976.  Anaerobe. 2012 18:523-9.
  • Costa, M., Sturgeon, A., Arroyo, L., Kim, P., Allen-Vercoe, E., Staempfli, H. and Weese, J.S. Comparison of the Fecal Microbiota of Healthy Horses and Horses with Colitis by High Throughput Sequencing of the V3-V5 Region of the 16S rRNA Gene. PLoS One. 2012;7(7):e41484.
  • Allen-Vercoe, E., Reid G, Viner N, O’Doherty K, Lee C, Hota S, Gloor G, Kim P, Vanner S, Weese S, and Petrof EO, “A Canadian Working Group Report on Fecal Microbial Therapy: Microbial Ecosystems Therapeutics” Canadian Journal of Gastroenterology, in press.
  • Allen-Vercoe, E. as part of The Human Microbiome Project Consortium. “A framework for human microbiome research” Nature. 2012 Jun 13;486 (7402):215-21 .
  • Allen-Vercoe, E. as part of The Human Microbiome Project Consortium. “Structure, Function and Diversity of the Human Microbiome in an Adult Reference Population” Nature. 2012 Jun 13;486(7402):207-14.
  • Castellarin, M., Warren, R.L., Freeman, J.D., Dreolini, L., Krzywinsky, M., Strauss, J., Barnes R., Watson, P., Allen-Vercoe, E, Moore, R.A and Holt, R.A. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma.  Genome Research. 2012 Feb;22(2):299-306.

The Human Microbiome Handbook


Critical reference explains strategies of microbiome research in humans. Summarizes the microbiome's effects on immunity, metabolism, genetics and psychology. Evaluates medical and nutritional therapies for modifying the microbiome. For healthcare researchers, nutritionists, microbiologists, and medical professionals. http://www.destechpub.com/product/human-microbiome-handbook/  

Complete publication list

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 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$350 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. 


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
Postdoctoral Fellow, 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
Postdoctoral Fellow, 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 .


Christian Carlucci

Dr. Christian Carlucci
Postdoctoral Fellow, NuBiyota

Christian is using the Roboguts and other models to predict the usefulness of potential therapeutic ecosystems against C.difficile infection.  
Motto: "People don't forget" 
Hobbies: Playing in a rock 'n' roll band 

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 Lachnospiracee 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. 
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

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



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! She is also involved in a current, long-term project to analyze the effects of various pulse foods on the gut microbiota, using the Roboguts. 
Motto: "Hakuna matata" 
Hobbies: Volleyball, addictive TV shows, more volleyball ...

Chris Ambrose

Chris Ambrose
Lab Manager

Chris does all the things that keep the lab running smoothly, including animal work, 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



Avery Robinson

Avery Robinson
Co-op student/Summer intern/Undergraduate project student

Avery is working to optimize the transformation efficiency of Fusobacterium nucleatum in preparation for construction of a transposon mutant library. Avery is also helping out with preparing strains and material for sending to our collaborators. 
Motto: Laugh, love, learn.
Hobbies: Reading, running, singing tunelessly, and being outside.


Simone Renwick

Simone Renwick
Co-op student/Undergraduate project student
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, to understand the role of these ecosystems in immune system activation. 
Motto: I can and I will. 
Hobbies: Reading, Hiking, Painting and Chess


Connor Gianetto-Hill

Connor Gianetto-Hill
Co-op student

Connor is working on optimizing Agrobacterium tumefaciens culture in bioreactor vessels in conjunction with Plantform.
Motto: "Adapt and overcome”
Hobbies: Netflix, reading, cooking, horror movies


Charley Carriero


Charley Carriero
NuBiyota Summer Intern

Charley is working with the NuBiyota team to help with NMR-based metabolic profiling of therapeutic ecosystems.



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.