Microbiology Services

University of Guelph, Agriculture & Food Laboratory (AFL) tests finished food products, raw ingredients, water and environmental samples to determine microbial growth including pathogen transmission risks in the farm-to-fork supply chain. We test a wide array of sample types: meat, poultry, fish, produce, dairy products, water, environmental swabs, and more. Our lab methods span the use of ‘gold-standard’ methods to novel and rapid techniques used to identify indicator organisms as well as pathogens such as Campylobacter, E.coli, Listeria, or Salmonella. Laboratory Services’ professional team of microbiologists and technologists is committed to providing the highest quality and value to our clients in laboratory support and testing programs.

Services Offered

Food and Water Microbiology

AFL can help you develop and validate analytical methods to detect, isolate, identify and characterize microorganisms in food, ingredients, water, and surface testing. We evaluate and validate test kits for detection and/or enumeration of microorganisms on many food type. In addition, we can also help monitor sanitation of equipment, food contact and plant environment surfaces for HACCP implementation.

Laboratory Services

Laboratory Services is accredited by the Standards Council of Canada for a variety of food and beverage types for many microbiological analyses on our Scope of Accreditation, including food-borne pathogens and enumeration requirements:

  • Total Bacterial Count
  • Total Coliform and E.coli Count
  • E. coli O157:H7
  • Staphylococcus aureus
  • Listeria monocytogenes
  • Salmonella spp.
  • Campylobacter spp.

Water Testing

Our water testing encompasses water from a variety of sources that can include potable water (tap, well), water used in food processing, surface water (pond, river, stream), irrigation/wash water, waste, recreational and recirculation water.   Our water microbial tests include:

  • E. coli/Total Coliform Enumeration
  • Heterotrophic Plate Count
  • Yeast and Mold Enumeration

AFL is licensed to provide microbial testing for drinking waters under Ont. Reg 318/319 and Ont. Reg. 170 for E.coli/Total coliforms and Heterotrophic Plate Count.

PLEASE NOTE: for Small Drinking Water Systems (SDWS), please contact us for appropriate testing and submission information.

Pathogen Identification and Detection

Have trouble identifying a bacterium? Send it to us! We have an impressive array of automated identification systems and microscopy methods to provide identification of organisms.

Yeast and Mold

This lab provides detection, enumeration, mold genus identification by microscopy examination, and molecular methods.

Method Development and Validation

This lab is accredited for method development and validation work. This lab has the expertise to work with clients to develop, adapt and/or validate new methods for various food and environmental matrices.

Shelf-life Studies and Challenge Studies

Shelf Life Studies

Shelf life studies help establish the longevity of the product before spoilage.  Food samples are stored over a non-accelerated time period and tested at pre-established time points based on the product ingredients. Our highly trained staff conducts microbiology tests that include standard spoilage organisms. Our Microbiology team will work with you to develop a scientifically sound sampling and testing protocol.

Challenge Studies 

Microbiological challenge testing has been, and continues to be, a useful tool for determining the ability of a food to support the growth of spoilage organisms or focusing on pathogens relevant to foods that need time/temperature control for safety. Microbiological challenge tests play an important role in the validation of processes that are intended to deliver some degree of lethality against a target organism or group of target organisms. Quite often, with this latter purpose, there is an associated performance standard that the process must deliver (for example, a 5-log reduction of Escherichia coli O157:H7 for fermented meats). We offer long-term sample storage and formal report for interpretive results as requested. 

Special Projects

  • Water, wastewater, soil and environmental samples
  • Environmental monitoring for food processing and farm environments
  • Analysis in support of your HACCP program
  • Bacterial, yeast and mold identification
  • Bacterial strain tracking in food processing plant environment
  • Pasteurization confirmation by alkaline phosphatase in milk and dairy products
  • Molecular based methods  


Rapid Methods

Using rapid detection platforms such as BAX (Hygiena) our scientists can identify the pathogens likely to make their way into food products, such as Salmonella, E. coli O157:H7 and Listeria monocytogenes. Cultural microbiology methods are also available and can be used for confirmatory testing. Rapid detection systems include:

  • Immunomagnetic Separation System, Dynal (Invitrogen)
    Salmonella spp. and E. coli O157:H7
  • BAX® PCR
    Listeria spp., L. monocytogenes,
    Salmonella spp., E. coli O157:H7
  • By ELISA
    Staphylococcus aureus enterotoxin

Routine Cultural Microbiology

Our testing is accredited for specific tests used on our Scope of Accreditation, including all bacterial food-borne pathogens and enumeration requirements including:

  • Aerobic Colony Count (ACC)
  • E. coli Count
  • Coliform Count
  • Campylobacter spp.
  • Listeria monocytogenes
  • Salmonella spp.
  • Staphylococcus aureus

We offer cultural methods following the Health Canada Compendium and participate in Canadian Food Inspection Agency (CFIA) proficiency testing programs.