- Agricultural microbiology: animal, food and soil microbiology
- Ecology of antibiotic resistance, functional biodiversity and phylogenetic biodiversity of Bacteria and Archaea in animal and plant production ecosystems
The theoretical approach of my research activities lies in the application of whole-community investigations (metagenomics) to elucidate the ecology of complex microbial communities in agricultural ecosystems. This is sustained by an experimental approach integrating complementary molecular and classical microbiology techniques in order to globally characterize the molecular and cellular microbial ecology of such communities and ecosystems.
We have initiated investigations in the area of bacterial ecology in the pre-harvest environment of animal and plant production, with a particular focus on the dynamics of antibiotic resistance and biodiversity in commensal anaerobic bacteria in swine production. It is known that, in the mammal gut, pathogens are largely outnumbered by commensals, which can both harbor antibiotic resistance genes, and that anaerobes dominate over aerobes in terms of abundance. Thus, it is hypothesized that anaerobic commensal bacteria constitute the numerically and ecologically dominant sub-population in the swine large intestine. The fundamental questions addressed by my research program are:
- How antibiotic additions to swine feed influence the occurrence of bacterial resistance to antibiotics in swine production?
- Which bacterial species and mobile genetic elements (plasmids, transposons, integrons) are involved in the dissemination of ecologically advantageous antibiotic resistance genes in swine production?
- What are the temporal evolution and geographical distribution of bacterial resistance to antibiotics in swine production?
Education and Experience
- Postdoctoral Fellow, INRS - Institut Armand-Frappier, Laval, QC, Canada, 2004-2007. Project: Fate of antibiotic resistance in an aerobic thermophilic biotreatment for swine waste.
- Ph.D. Microbiology, McGill University, Montreal, QC, Canada, 2000-2004. Project: Impact of seasonal variations, nutrients, pollutants and dissolved oxygen on the microbial composition and activity of river biofilms.
- Research Officer – Microbiologist, Sodexen, Laval, QC, Canada, 1998-1999. Project: Optimization of an aerobic biotreatment of PAH-contaminated soils in a bioreactor.
- Microbiologist, Buckman Laboratories of Canada, Vaudreuil-Dorion, QC, Canada, 1996-1998. Project: Pulp and paper microbiology.
- M.Sc. Applied Microbiology, INRS - Institut Armand-Frappier, Laval, QC, Canada, 1994-1996. Project: Study of pentachlorophenol biodegradation in aerobic and anaerobic conditions.
- B.Sc. Microbiology, Laval University, Quebec City, QC, Canada, 1991-1994.
Funding and Collaborations
- Ngadi M, Chénier MR (2012-2014) Shelf life extension for preformed pizza using pulsed ultraviolet light, MAPAQ - Programme de soutien à l’innovation en agroalimentaire.
- Chénier MR, Whalen JK, Whyte LG, Séguin P (2010-2013) Evaluation of Bacterial and Archaeal DNA for optimizing N-fertilizer applications in maize agroecosystems in Quebec, FQRNT – Team Research Projects Program.
- Bede J, Driscoll BT, Whyte LG, Chénier MR (2010-2011) Multipurpose microplate reader, NSERC - Research Tools and Instruments.
- Chénier MR (2009-2014) Bacterial antibiotic resistance in swine production, CFI - Leaders Opportunity Fund (funding for equipment).
- Chénier MR (2009-2014) Antibiotic resistance in food production, NSERC - Discovery Grants.
Pakpour S, Milani AS, Chénier MR (2012) A multiple-criteria decision-making approach for comparing sample preservation and DNA extraction methods from swine feces. American Journal of Molecular Biology, 2(2):159-169.
Pakpour S, Jabaji S, Chénier MR (2012) Frequency of antibiotic resistance in a swine facility 2.5 years after a ban on antibiotics. Microbial Ecology 63:41-50.
Hussain SA, Prasher SO, Chénier MR, Arya G (2011) Removal of nitrate-N by antibiotic-exposed bacterial isolates from a constructed wetland. World Journal of Microbiology and Biotechnology, 27:2061-2069.
Chénier MR, Juteau P (2009) Impact of an aerobic thermophilic sequencing batch reactor on antibiotic-resistant anaerobic bacteria in swine waste. Microbial Ecology, 58:773-785.
Chénier MR, Juteau P (2009) Fate of chlortetracycline- and tylosin-resistant bacteria in an aerobic thermophilic sequencing batch reactor treating swine waste. Microbial Ecology, 58:86-97.
Chénier MR, Beaumier D, Roy R, Driscoll BT, Lawrence JR, Greer CW (2006) Influence of nutrient inputs, hexadecane and temporal variations on nitrification and exopolysaccharide composition of river biofilms. Canadian Journal of Microbiology, 52(8): 786-797.
Chénier MR, Beaumier D, Fortin N, Roy R, Driscoll BT, Lawrence JR, Greer CW (2006) Influence of nutrient inputs, hexadecane and temporal variations on denitrification and community composition of river biofilms. Applied and Environmental Microbiology, 72(1):575-584.
Lawrence JR, Chénier MR, Roy R, Beaumier D, Fortin N, Swerhone GDW, Neu TR, Greer CW (2004) Microscale and molecular assessment of impacts of nickel, nutrients and oxygen level on structure and function of river biofilms. Applied and Environmental Microbiology, 70(7):4326-4339.
Chénier MR, Beaumier D, Roy R, Driscoll BT, Lawrence JR, Greer CW (2003) Impact of seasonal variations and nutrient inputs on nitrogen cycling and degradation of hexadecane by replicated river biofilms. Applied and Environmental Microbiology, 69(9):5170-5177.
- Ms. Sepideh Pakpour (October 2010-April 2011) A multiple-criteria decision-making approach for comparing sample preservation methods and DNA extraction techniques from swine feces.
- Ms. Ruvana Fonseka (January-December 2010) Effect of solid media composition on the enumeration of total anaerobic bacteria in swine feces.
- Dr. Snizhana V. Olishevska (July 2011-Octobeer 2012) Evaluation of biochar soil amendments in reducing soil and water pollution from antibiotics and pathogens in poultry manure. Co-supervised with Dr. Shiv O. Prasher, Department of Bioresource Engineering.
- Mr. Devin Holman (2009- ) Impact of antibiotic use in swine production on the development of bacterial resistance to antibiotics. Scholarships: McGill - Provost’s Graduate Fellowship, $5,000, Fall 2009; Centre de recherche en infectiologie porcine - Bourse de dépannage, $6,000, July 1st to October 31st, 2010; FQRNT- MITACS Internship Program, $10,000, March to June 2011; Travel Stipend for the Canadian Swine Health Forum, 3-4 November 2011, Niagara Falls, ON, Canada; Centre de recherche en infectiologie porcine - Bourse de congrès, $1,770, for the Annual Meeting of the Canadian Society of Microbiologists, 20-23 June 2012, Vancouver, BC, Canada.
- Ms. Hanadi Al-Sawawi (2008-2010) Characterization of a thermophilic Thermobifida fusca isolate and its galactosidase. Co-supervised with Dr. Benjamin K. Simpson, Department of Food Science.
- Mr. Adrian Prado (2012- ) Evaluation of Bacterial and Archaeal DNA for optimizing N-fertilizer applications on canola agroecosystems in Quebec. Co-supervised with Dr. Lyle G. Whyte, Department of Natural Resource Sciences - Microbiology Unit.
- Ms. Tina Mohammadbeygy (2012- ) Shelf life extension for preformed pizza using pulsed ultraviolet light. Co-supervised with Dr. Michael Ngadi, Department of Bioresource Engineering.
- Mr. Navjot Banghu (Summer 2012) Optimization of antibiotic extraction and HPLC quantification techniques in swine feed. Research project for M.Sc. Non-Thesis.
- Mr. Shoieb Akaram Ismail (2010-2012) Evaluation of biochar soil amendments in reducing soil and water pollution from pathogens in poultry manure. Co-supervised with Dr. Shiv O. Prasher, Department of Bioresource Engineering.
- Mr. Philippe LeBel (2010-2012) Impact of mash feed on Salmonella carriage in swine. Co-supervised with Dr. Ann Letellier, University of Montreal, Faculty of Veterinary Medicine, Department of Pathology and Microbiology.
- Ms. Sepideh Pakpour (2008-2010) Detection of antibiotic resistance in swine production. Scholarships: McGill - Principal’s Graduate Fellowship, $2,500, Fall 2008; McGill - Principal’s Graduate Fellowship, $2,500, Fall 2009; McGill - Macdonald Class Of '44 Rowles, $750, Fall 2009; NSERC - Alexander Graham Bell Canada Graduate Scholarship M, $17,500, May 2009 - April 2010.
- Ms. Karen Villarmino (fall 2011) Optimization of protocols for classical and molecular microbiology.
- Ms. Élise Denis (fall 2011-winter 2012) HPLC quantification of antibiotics in swine feed. Co-supervised with Dr. Kebba Sabally, School of Dietetics and Human Nutrition.
- Ms. Shakira Fulton-McLean (summer 2011) Optimization of end-point PCR for Archaea in swine feces.
- Ms. Vivian Chan (summer 2011) Optimization of end-point PCR for Bacteria in swine feces. NSERC-USRA, $4,500.
- Mr. FengYang Wang (fall 2010-summer 2011) Enumeration of total, chlortetracycline-resistant and tylosin-resistant microbial populations at the Swine Complex.
- Ms. Maryse Charlebois (2009-2010) Co-supervised with Dr. Grant Clark, Department of Bioresource Engineering.
- Ms. Cloé Rainville (2009) Co-supervised with Dr. Shiv O. Prasher.
- Ms. Nema Boulis (summer 2009) Temporal evolution of the abundance of anaerobic bacterial populations in swine waste. NSERC-USRA, $4,500.
- Ms. André-Anne Rouleau (fall 2008-winter 2009).
- Member of the Education and Careers Committee of the Canadian Society of Microbiologists (2012- ).
- Member of the Scientific Committee of Fondation Initia (2011- ).
- Member of the Academic Program Committee of the Faculty of Agricultural and Environmental Sciences (2010-2013).
- Section Vice-Chair (2008-2010) and Chair (2010-2012) of the Molecular Genetics and Cellular Microbiology Section of the Canadian Society of Microbiologists.
- Member (2008-2010) and Chair (2010-2013) of the Library Committee of the Faculty of Agricultural and Environmental Sciences.
- Reviewer for scientific journals: Canadian Journal of Microbiology (since 2005, French and English manuscripts), Microbial Ecology (since 2009), Applied Microbiology and Biotechnology (since 2010), Journal of Applied Microbiology (since 2010), Journal of Food Engineering (since 2010), Letters in Applied Microbiology (since 2011), Science of the Total Environment (since 2011).
- Reviewer for funding agencies: Alberta Livestock and Meat Agency - Agriculture Funding Consortium Program (since 2009), NSERC - Discovery Grants Competition (since 2010).