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Microbiomes in Humans, animals and the Environment


Unraveling the Role of Microbiomes in Health and Disease

Toward Microbiota Ecosystem Engineering

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Microbiomes in Humans, animals and the Environment


Unraveling the Role of Microbiomes in Health and Disease

Toward Microbiota Ecosystem Engineering

Welcome to my Lab

I'm an Associate Professor of Microbiome Science at the University of Manitoba, Canada. Using cutting-edge sequencing technologies, coupled with bioinformatics and advanced statistical and mathematical approaches, my aim is to advance human and animal health through an improved understanding of composition and function of microbial communities present in the gut, the vaginal tract, and the mammary system. I'm also working closely with a diverse group of researchers to characterize microbial communities in other environments, such as manure digesters, compost, soil, and water, in order to address ecologically important questions. With funding support from "Canadian Foundation for Innovation" (CFI) my laboratory has become one of the most advanced of its kind and provides state-of-the-art training in microbiome research. 

In my research, I’m interested to map the dynamics of microbiome and its metabolome, identify factors that impact the metabolic capacity of microbiome and its synergetic relationship with the host, and understand the mechanisms through which microbiome and metabolome impacting the host health and disease status. Understanding these interactions across multiple biological levels allow development and subsequent testing of strategies to improve humans or animals health in a personalized fashion. The fundamental questions I address throughout my research include, a) What shifts occur in the compositional and functional diversity of microbiome of humans/animals during specific health disorders? b) What shifts occur in the metabolomic profile of such individuals? c) Which species are contributing to the functional shifts in microbiome and resultants metabolomic profiles? d) Can the microbiome or mtabolomic profiles be used as a diagnostic/prognostic tool? d) Can the balance of microbiome be retained through application of specific supplements including pre- and probiotics? e) What are the modes of action of existing pre- and probiotics and how can we develop new probiotic targets to further improve gut/host health? f) How lifestyle interacts with individual’s genetics, gut microbiome and metabolomic phenotype? and g) How these interactions are related to risk factors for chronic conditions?

My research is multidisciplinary and involves collaborations with teams of human and animal nutritionists, gastroenterologist, immunologists, reproductive physiologists,  microbiologists, kinesiologists, nurses, clinicians, epidemiologists, biostatisticians, and chemists as well as animal, plant and soil scientists. I'm affiliated with below organizations:

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Projects


Projects


projects

My projects can be boiled down into five categories: 

  1. Factors that are impacting the early development of gut microbiota in humans and animals (e.g. mode of delivery, vaginal microbiome, milk microbiome, antibiotics).
  2.  Human and animals non-communicable diseases that we believe are linked to the lifestyle factors (e.g. diet, physical activity, stress, sleep) and changes in the ecology of our indigenous microbiome  (e.g inflammatory bowel disease, obesity, type 2 diabetes, and cardiovascular disease in humans; acidosis, subacute ruminal acidosis, milk fat depression, and mastitis in ruminants). Microbiome-Gut-Brain axis and enterohepatic pathway play important roles in host-microbiome interactions. 
  3. Infectious diseases that are associated with dysbiotic microbiota (e.g. neonatal and post-weaning diarrhea in piglets, Johnes disease and mastitis in ruminants).
  4. Systematic development of new probiotic targets and intervention strategies for manipulation of microbiota and microbiota ecosystem engineering (e.g. probiotics, probiotics, fecal transplant, mini-microbiome development).
  5. Role of microbial communities in other environment (e.g. compost, soil, water).
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REAL-TIME MICROSCOPY, CULTUROMICS, METAGENOMICS AND METATRANSCRIPTOMICS


From Van Leeuvenhoek microscopy and Hungate anaerobic culturing to high throughput sequencing

REAL-TIME MICROSCOPY, CULTUROMICS, METAGENOMICS AND METATRANSCRIPTOMICS


From Van Leeuvenhoek microscopy and Hungate anaerobic culturing to high throughput sequencing

Microbiome and Large Animal Biosecurity Laboratory

Microscopy

My laboratory supports real-time microscopy-based research that allows visualization of the process by which bacteria invade eukaryotic cells, as well as traditional microscopy-based research, such as Fluorescent In Situ Hybridization (FISH) analysis.

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HIGH-THROUGHPUT SEQUENCING

The illumina sequencing platform and associated bioinformatic workstations support metagenomics and metatranscriptomics studies for understanding the composition and function of microbial communities.

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AEROBIC AND ANEROBIC CULTURING

Aerobic and anaerobic culturing are an integral component of my research which allow us to systematically target, culture and study the cultivable or yet uncultivable members of the microbial communities. 

All animal research in this facility are conducted in accordance to the guidelines of Canadian Council on Animal Care and are overseen by the University of Manitoba Senate Committee on Animal Care and Animal Care Protocol Management and Review Committee.

Immunological and metabolomic studies

Immunological aspects of host-microbiome interactions are studied either independently or in collaboration. Metabolomics components of my research are conducted in collaboration. 

Large Animal Biosecurity Laboratory

The Large Animal Biosecurity Laboratory includes level II containment infrastructures and animal rooms that facilitate micobiome research on farm animals. We have also capability to run pre-clinical trials using animals as a model for human diseases.  

My laboratory at University of Manitoba is supported by grants from Canadian Foundation for Innovation.