Principal Investigator


Managerial Team

SHADI SEPEHRI, General Manager

HOOMAN DERAKHSHANI, Manager of the Sequencing Platform

SHIRIN MOOSSAVI,  Journal club coordinator


Research Staff

Dr. Shadi Sepehri

Shadi Sepehri, MD, PHD, FCCM, D(ABMM), Research Scientist

Shadi is a board-cetrified Clinical Microbiologist with research interest in novel applications of molecular techniques in diagnostic microbiology. She earned her MD from Mashhad University of Medical Sciences in Iran and her PhD in Medical Microbiology at the University of Manitoba, Canada. Following her PhD and a brief post-doctoral training at St. Boniface Research Centre, she entered a Clinical Microbiology Fellowship Training Program at the University of Manitoba, and following completion became a certified diplomat of the American Board of Medical Microbiology (ABMM) and a fellow of the Canadian College of Microbiologists (FCCM) in 2014. She is a Reserach Scientist at the Children's Hospital Research Institute of Manitoba (CHRIM) and the general manager of Gut Microbiome Laboratory. All questions with regard to the samples shipment and ordering reagents should be directed to Dr. Sepehri.

 

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TERRY ZhANG, MSC, PHD, POST-DOCTORAL FELLOW

Terry received his BSc from Henan University of Technology, China, his MSc from University of Reading, UK, and his PhD from Manchester Metropolitan University, UK all in Food Science. Terry's research interest is on immune stimulating properties of fiber. He is currently involved in several projects on different aspects of microbiome-host cross talks with specific attention to the role of fiber and dietary enzymes on manipulation of gut environment, bile acids profile and host metabolism and immune response.

 

 

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HOOMAN DERAKHSHANI, DVM, MSC, PHD, Post-doctoral fellow

Hooman received his DVM degree from the University of Tehran, Iran and his MSc in Animal Science from The University of Queensland, Australia. Hooman's PhD project was focused on the "Dynamics of mammary microbiome and mycobiome in dairy cows and their associations with mastitis". Hooman is currently working on a number of projects investigating the inter-related physio-ecology of the gut, the mammary glads and the vaginal tract in ruminants, monogastrics and humans. He is also in charge of the sequencing platform and has extensive experience in bioinformatics and statistical analyses of large sequencing data.

 

KELSEY FEHR, MSC, Research Technician

Kelsey received her BSc in Animal Science from the University of Manitoba. Her MSc project at my laboratory was focused on "The effects of organic and inorganic bedding materials on udder health and milk microbiome of dairy cows". She is currently working on a number of projects investigating the inter-related physio-ecology of the rumen and hindgut, the mammary glads and the vaginal tract. She has also extensive experience in high-throughput sequencing, and bioinformatics and statistical analyses of data.

 

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Zhangbin Cai, MSC, Research Technician

Zhangbin obtained his BSc in Animal Science from Dalhousie University. His MSc project in my laboratory was focused on "Survivability and infectivity of Porcine Epidemic Diarrhea virus (PEDv) in different environment and new disinfectants against it". Zhangbin has extensive experience in cell culture, and DNA- and RNA-based molecular techniques. He is involved in a number of projects focusing on the role of microbiomes in health and disease.

 


PHD Students

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ELNAZ AZAD, DVM, DVSC, PHD STUDENT, JOINT WITH TIM MCALLISTER

Elnaz received her DVM and later her DVSc in Surgery from University of Tehran, Iran. The focus of her PhD project is on understanding the role of rumen microbiome as a predisposition factor to bloat in grazing cattle. This project is a collaborative work between University of Manitoba and Agriculture Agri-Food Canada Lethbridge Research Centre. During this project Elnaz is exposed to 16S based microbiome analyses, prediction of functional metagenome as well as metatranscriptomics analyses.

 

 

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SHIRIN MOOSSAVI, MD, MSC, PHD STUDENT

Shirin has obtained her Medical Doctorate from Tehran University of Medical Sciences, Iran, and her MSc in Genetic Manipulation and Molecular Biology from University of Sussex, UK. Before joining my lab, she was coordinating several projects at the Digestive Disease Research Institute (DDRI), Tehran University of Medical Sciences, Iran. Shirin is interested in factors shaping the human microbial communities and physico-chemical alterations underlying microbial community dysbiosis. She is currently studying milk microbiota in Canadian Healthy Infant Longitudinal Development (CHILD) and stool microbiota in The Manitoba Personalized Lifestyle Research (TMPLR) programme.”

 

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HamiD Khalouei, MSc, PHD STUDENT

Hamid received his MSc in Ruminant Nutrition from the University of Tehran, Iran. Hamid's PhD project is focused on "Understanding the mechanism of action of Saccharomyces cervicea fermentation products in stabilization of rumen environment during subacute ruminal acidosis". Hamid uses a series of Omics methodologies including metabonomics to tackle this question.

 

 

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Junfei Guo, BSc, MSc & PHD in Vet Med, PHD STUDENT

Junfei received her BSc, MSc and PhD in Veterinary Medicine from Nanjing Agricultural University, China. She has extensive experience in large animal surgery as well as in molecular biology. Junfei is currently working toward her second PhD degree which is focused on understanding the mode of action of Saccharomyces cervicea fermentation products on dairy cows health. She is using 16S rRNA gene sequencing, transcriptomics, metatranscriptomics, and an array of immunological assays to study microbiome-host interactions. 

 


MSC Students

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JULE DUBE-SMITH, MSC STUDENT

Julie received his BSc in Chemistry from the University of Manitoba. His MSc project focuses on "Understanding the composition and function of microbial community of compost tea products to determine the effectiveness of applying compost tea incorporated into both conventional and organic management practices in a commercial potato cropping system". He is applying 16S rRNA-based microbiome, and ITS-based mycobiome analyses to evaluate the function of microbial communities and their interactions with the plant.

 


Medical and Undergrad Students

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TSU-Yu (Unice) Chang, BSC, Medical Student

Unice received her BSC in Biochemistry from McGill University. She is currently a third year Medical student at the University of Manitoba. She was involved in collection of data and gut microbiome analysis of subjects enrolled in the Manitoba Personalized Lifestyle Research (TMPLR) program; and continues to work with my group on a number of projects focusing on the role of fiber and artificial sweeteners on the composition and functional capacity of gut microbiome.

 

 

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Jimena Montenegro Gonzalez, Fourth year undergrad

Jimena is a fourth year undergrad student in Animal Science at the University of Manitoba. During the course of summer, Jimena got exposed to aerobic and anaerobic culturing of bacteria, molecular microbiology techniques such as PCR amplification and high-throughput Illumina sequencing, and optimization of several challenge models in swine. She continues to work with my group to study the effects of stressors on the physio-ecology of the piglet gut.

 

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LindsAy Ironside, Third year undergrad

Lindsey is a third undergrad student in Microbiology at the University of Manitoba. During the course of summer, she was involved in collection of data and samples from subjects enrolled in the Manitoba Personalized Lifestyle Research (TMPLR) program. Also in the lab, she got exposed to aerobic and anaerobic culturing of bacteria, and molecular microbiology techniques such as DNA extraction and PCR amplification. She continues to work part-time with the TMPLR throughout the academic year.

 

 

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Hannah Keenes, Second year undergrad

Hannah is a second year undergrad student in Animal Science at the University of Manitoba. Hannah has got training in aerobic and anaerobic culturing of bacteria, molecular microbiology techniques such as PCR amplification and high-throughput Illumina sequencing, and optimization of several challenge models in swine. Together with Jimena, they study the effects of stressors on the physio-ecology of the piglet gut.

 

 

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Kailey Fontaine, Fourth year undergrad

Kailey is a fourth year undergrad student in Animal Science at the University of Manitoba. She is currently involved in development of reading materials for undergrad students on the inter-related physio-immuno-ecology of the gastrointestinal tract. She is also involved in the analyses of microbiome data and studies investigating the role of microbiome in gut health of monogastric species. 


Lab affiliates

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Azin Khafipour, BSC, MSC, Research Technician with Nazim Cicek, Biosystems Engineering

Azin has a BSc in Information Technology. She obtained her MSc in Immunology from University of Manitoba studying host-microbiome interactions in an animal model of inflammatory bowel disease . She is currently studying microbiota behaviour and dynamics in bioreactors to generate knowledge toward bioengineering of microbial ecosystems.

 

 

Leila Kamino, Plant Science, University of Manitoba, PhD student with Rob Gulden

The role of crops and weeds on soil function – the case of extracellular DNA (eDNA) persistence.

 

RUIDONG MI, SOIL SCIENCE, UNIVERSITY OF MANITOBA, MSC STUDENT WITH ANNEMIEKE FARENHORST ADN AYUSH KUMAR

A survey of microbial compositions and antibiotic resistant genes in drinking water in four First Nation communities in the province of Manitoba.

 

SAMAR AHMED, HUMAN NUTRITIONAL SCIENCE, UNIVERSITY OF MANITOBA, Phd STUDENT WITH JAMES FRIEL

Short and long-term impacts of artificial sweeteners on gut microbiome composition and function.

 

MOHAMMAD FAZLE ALAM RABBI, IMMUNOLOGY, UNIVERSITY OF MANITOBA, PHD STUDENT WITH JEAN-ERIC GHIA

The impact of human catestatin on gut microbiota dysbiosis in a DSS-colitis mice model.

 

ELSIE JORDAAN, BIOSYSTEM ENGINEERING, UNIVERSITY OF MANITOBA, PHD STUDENT WITH NAZIM CICEK

Microbial communities of anaerobic digesters fed dairy and swine manure.

 

SAYMORE NDOU, ANIMAL SCIENCE, UNIVERSITY OF MANITOBA, PHD STUDENT WITH MARTIN NYACHOTI

Production, absorption, and metabolic consequences of fatty acids in growing pigs fed fibrous diets: The impact on intestinal microbiome composition and function.

 

ETHENDHAR RAJENDIRAN, HUMAN NUTRITIONAL SCIENCE, UNIVERSITY OF MANITOBA, PHD STUDENT PETER JONES

Understanding the impact of saturated fats from dairy on circulating lipids and gut microbiome composition and function in healthy humans.