Course coordinator
Professor Mark Turner
Consultation is by appointment. To make an appointment, please email.
Course overview
- Study period
- Semester 1, 2025 (24/02/2025 - 21/06/2025)
- Study level
- Postgraduate Coursework
- Location
- St Lucia
- Attendance mode
- In Person
- Units
- 2
- Administrative campus
- St Lucia
- Coordinating unit
- Agriculture and Food Sustainability School
Examines the positive (fermentation) and negative (spoilage) roles microbes play in foods and methods of preservation. Rapid detection methods and molecular (DNA) methods relevant to food microbiology including genomics (WGS), real-time PCR and culture-independent identification are investigated. It also explores spores, biofilms and problems and applications of bacteriophages, GM microbes and bioreactors. Practical components include organic acid preservation of yeast in apple juice, extension of shelf-life using carbon dioxide, decimal reduction of bacteria using heat, the isolation and identification of food bacteria using 16s rDNA PCR, DNA sequencing and bioinformatics.
Food Microbiology & Biotechnology (MICR7001) is a diverse course in applied microbiology which explores a range of topics including: food spoilage, preservation, fermentation (including precision fermentation and microbes as alternative protein),ﾠ bacteriophages (CRISPR-Cas defense systems), rapid detection methods, bacterial identification using DNA sequencing (Sanger and next-generation sequencing), whole genome sequencing for tracking the source of foodborne outbreaks, spores, biofilms, biocontrol, GM microbes, bioreactors and bacterial stress responses. The course will have practicals in the first half of semester and then tutorials in the other half of semester (i.e. it won't have tutorials and practicals in the same week). The tutorials will look at culture-independent analysis of bacterial populations from different food samples and will allow time to work on an assignment where you will analyse and interpret bacterial community DNA sequence data obtained from food samples. The practicals will involve wet-lab work that closely align with the topics covered during the lectures. The 2 main textbooks used in this course are electronic books (e-books) available free for students through the UQ library.ﾠ
Course requirements
Assumed background
An understanding of basic microbiology through completion of a previous course in microbiology (or food microbiology) is preferred, but not essential.
Incompatible
You can't enrol in this course if you've already completed the following:
MICR3860 (co-taught)
Course contact
Course staff
Lecturer
Professor Mark Turner
Dr Yosephine Gumulya
Timetable
The timetable for this course is available on the UQ Public Timetable.
Aims and outcomes
1. Analyze the mechanisms by which microorganisms cause food spoilage or be useful in fermentation, and develop plans to effectively detect foodborne microbes using rapid methods.
2. Evaluate the basis of molecular techniques and their use in tracking foodborne outbreaks and other food applications.
3. Demonstrate an understanding of techniques to effectively work in a food microbiology laboratory using cultural and molecular methods
4. Describe how culture-independent bacterial community analysis works and how to intepret the results for such analyses using bioinformatics.
Learning outcomes
After successfully completing this course you should be able to:
LO1.
Describe how microorganisms can cause food spoilage and be useful using fermentation.
LO2.
Determine and how we can control and detect food microbes quickly using rapid methods.
LO3.
Evaluate the protocols as well as strengths and weaknesses of culture-based and molecular methods for the microbiological analysis of foods.
LO4.
Describe the basis of molecular techniques (e.g. whole genome sequencing) and their use in tracking foodborne outbreaks and other food applications.
LO5.
Carry out bacterial community DNA sequence analysis and interpret the results.
LO6.
Explore and analyse bacterial spores, biofilms and bacterial stress responses and the impacts they can have on food processing.
LO7.
Describe how microbes and bioreactors are utilised for the production of food or food ingredients.
Assessment
Assessment summary
| Category | Assessment task | Weight | Due date |
|---|---|---|---|
| Examination |
In-semester exam
|
30% |
9/04/2025 2:00 pm
Week 7 - during Lecture time Venue: Bldg 11A - Room 110/111 |
| Tutorial/ Problem Set |
Culture-independent analysis of food bacteria
|
25% |
29/05/2025 2:00 pm |
| Examination |
Final Examination
|
45% |
End of Semester Exam Period 7/06/2025 - 21/06/2025 |
A hurdle is an assessment requirement that must be satisfied in order to receive a specific grade for the course. Check the assessment details for more information about hurdle requirements.
Assessment details
In-semester exam
- Identity Verified
- In-person
- Mode
- Written
- Category
- Examination
- Weight
- 30%
- Due date
9/04/2025 2:00 pm
Week 7 - during Lecture time
Venue: Bldg 11A - Room 110/111
Task description
This exam will examine knowledge and understanding of material delivered in specific lectures.
It will consist of multiple-choice and short answer/essay questions.
This assessment task is to be completed in-person. The use of generative Artificial Intelligence (AI) or Machine Translation (MT) tools will not be permitted. Any attempted use of AI or MT may constitute student misconduct under the Student Code of Conduct.
Exam details
| Planning time | no planning time minutes |
|---|---|
| Duration | 90 minutes |
| Calculator options | (In person) Casio FX82 series only or UQ approved and labelled calculator |
| Open/closed book | Closed Book examination - no written materials permitted |
| Exam platform | Paper based |
| Invigilation | Invigilated in person |
Submission guidelines
Deferral or extension
You may be able to defer this exam.
Culture-independent analysis of food bacteria
- Mode
- Written
- Category
- Tutorial/ Problem Set
- Weight
- 25%
- Due date
29/05/2025 2:00 pm
- Other conditions
- Student specific.
Task description
Many microbes that are alive in foods are unable to be cultured using standard laboratory techniques. With the explosion of next generation sequencing, culture-independent methods have become accessible for identifying the population of bacteria at a very deep level. The purpose of this assessment item is to examine your ability to analyse, using culture-independent analysis methods, the bacterial populations in foods and to interpret the results. An introduction lecture will be given in the tutorial session and several examples of research papers using this technique in foods will be provided.
You will be given a set of data and information which you will analyse and provide a summary of the results in a report. You will also interpret the results in the wider field of food microbiology and cite relevant references. The samples you will be provided will be from different foods at different stages of shelf-life which have undergone different treatments. The word limit and specific details of the assessment will be provided in the tutorial class. You will have time during the tutorials to carry out this analyses and write the report. You may ask the lecturer for guidance/assistance during these sessions.
While you can work in a small group, a report describing the work and analysis of results will be submitted by individual students (not a group).
Any copying of text from other sources, including other student's reports, will be considered plagiarism and reported to the School Integrity Officer.
This task has been designed to be challenging, authentic and complex. Whilst students may use AI and/or MT technologies, successful completion of assessment in this course will require students to critically engage in specific contexts and tasks for which artificial intelligence will provide only limited support and guidance.
A failure to reference generative AI or MT use may constitute student misconduct under the Student Code of Conduct.
To pass this assessment, students will be required to demonstrate detailed comprehension of their written submission independent of AI and MT tools.
Submission guidelines
You must submit your Assessment task, in Blackboard, via the Turnitin link by the submission deadline. You should also retain an electronic copy of every piece of assessment you submit.
Legal Declaration
By submitting your work via this website, you formally declare that (1) it is your own original work, and no part of the work has been copied from any other source or person except where due acknowledgement is made; (2) no part of the work has been previously submitted for assessment in this or any other institution; and (3) you have read the UQ Academic Integrity and Plagiarism Policy (http://ppl.app.uq.edu.au/content/3.60.04-student-integrity-and-misconduct) and understand its implications.
Deferral or extension
You may be able to apply for an extension.
Late submission
A penalty of 10% of the maximum possible mark will be deducted per 24 hours from time submission is due for up to 7 days. After 7 days, you will receive a mark of 0.
Final Examination
- Hurdle
- Identity Verified
- In-person
- Mode
- Written
- Category
- Examination
- Weight
- 45%
- Due date
End of Semester Exam Period
7/06/2025 - 21/06/2025
Task description
The final exam will contain a mix of short answer and short essay questions.
Students must attend the end of semester exam in person, it will be held on-campus. Have your UQ student ID card available for all your exams.
This assessment task is to be completed in-person. The use of generative Artificial Intelligence (AI) or Machine Translation (MT) tools will not be permitted. Any attempted use of AI or MT may constitute student misconduct under the Student Code of Conduct.
Hurdle requirements
Refer to Additional Course Grading Information / Course Grading Rules and Assessment Hurdles for details on the hurdle.Exam details
| Planning time | 10 minutes |
|---|---|
| Duration | 120 minutes |
| Calculator options | (In person) Casio FX82 series only or UQ approved and labelled calculator |
| Open/closed book | Closed Book examination - no written materials permitted |
| Exam platform | Paper based |
| Invigilation | Invigilated in person |
Submission guidelines
Deferral or extension
You may be able to defer this exam.
Course grading
Full criteria for each grade is available in the Assessment Procedure.
| Grade | Description |
|---|---|
| 1 (Low Fail) |
Absence of evidence of achievement of course learning outcomes. Course grade description: 0 - 34% |
| 2 (Fail) |
Minimal evidence of achievement of course learning outcomes. Course grade description: 35% - 46% |
| 3 (Marginal Fail) |
Demonstrated evidence of developing achievement of course learning outcomes Course grade description: 47% - 49% OR failure to meet course hurdle requirement. |
| 4 (Pass) |
Demonstrated evidence of functional achievement of course learning outcomes. Course grade description: 50% - 64% |
| 5 (Credit) |
Demonstrated evidence of proficient achievement of course learning outcomes. Course grade description: 65% - 74% |
| 6 (Distinction) |
Demonstrated evidence of advanced achievement of course learning outcomes. Course grade description: 75% - 84% |
| 7 (High Distinction) |
Demonstrated evidence of exceptional achievement of course learning outcomes. Course grade description: 85% - 100% |
Additional course grading information
COURSE GRADING RULES AND ASSESSMENT HURDLES:
Students must score a passing grade in the Final Exam to pass this course.
If a student obtains an overall percentage greater than the cut-offs set to achieve a 4 or higher for the course based on marks from a combination of progressive assessment and the final exam and the student does NOT score a pass mark for the Final Exam, they are unable to achieve a grade higher than a 3 (failing grade) for the course.
Supplementary assessment
Supplementary assessment is available for this course.
Additional assessment information
Assignment writing
You must not re-use past work from previous assessments in your assignments. You are encouraged to:
- read the instructions for assignments carefully and ensure that you address all the requirements,
- refer to references both in the readings and beyond, and cite references in the appropriate manner,
- reflect on your own experience and provide insight and critical thinking,
- write clearly and concisely.
Turnitin Assignments
Assignments that are required to be submitted through TurnItIn, must only be uploaded to the assessment specific Turnitin link on the relevant course Blackboard site. ﾠIf you submit any version of your assessment item to any other Turnitin link, this is considered cheating, and you will be held liable for this action.
Release of marks
Unless specifically indicated by the course coordinator, every attempt will be made to have the results for progressive assessment available within 3 weeks of submission. For items of assessment submitted in the last 2 weeks of the semester, the results will not be available until grades release day. Results and feedback availability will be advised to you by email or announced via the course Blackboard site.
Re-mark Applications – refer to the University's Re-mark Policy to check your eligibility.
Remark applications will not be considered without first having contacted your Course Co-ordinator.
Information for students can be found at : https://my.uq.edu.au/information-and-services/manage-my-program/exams-and-assessment/querying-result
Deferred and Supplementary assessment (including Deferred Examinations)
Deferred and Supplementary information can be located on the my.UQ website
Learning resources
You'll need the following resources to successfully complete the course. We've indicated below if you need a personal copy of the reading materials or your own item.
Library resources
Find the required and recommended resources for this course on the UQ Library website.
Additional learning resources information
Lecture notes will be available on the course Blackboard site.
Lectures will be recorded. Some tutorials will be recorded, specifically introductory explanations to the assessment.
You will need to bring your own laboratory coat and safety glasses to all practical classes - these can be purchased from the UQ Book Shop. You must also make sure that you wear shoes that cover your feet (ie. no thongs or sandals) for all practical classes. If you fail to meet these requirements, you will not be allowed to participate in practical classes.ﾠ
Learning activities
The learning activities for this course are outlined below. Learn more about the learning outcomes that apply to this course.
Filter activity type by
Please select
| Learning period | Activity type | Topic |
|---|---|---|
Multiple weeks From Week 1 To Week 13 |
Lecture |
Course material delivery Lectures containing the course material will be delivered each week on various topics. In these lectures there may be activities and discussions. |
Multiple weeks From Week 1 To Week 6 |
Practical |
Hands-on experiments. There will be 3 hour practicals which will give you technical skills in a number of different food microbiology related experiments. These will run in half the semester with tutorials in the other half. |
Multiple weeks From Week 8 To Week 12 |
Tutorial |
Culture-independent bacterial community analysis You will learn about culture-independent bacterial community analysis and how to interpret the results. Time will also be provided for you to carry out the assignment. These will run in half the semester with practicals in the other half. |
Policies and procedures
University policies and procedures apply to all aspects of student life. As a UQ student, you must comply with University-wide and program-specific requirements, including the:
- Student Code of Conduct Policy
- Student Integrity and Misconduct Policy and Procedure
- Assessment Procedure
- Examinations Procedure
- Reasonable Adjustments - Students Policy and Procedure
Learn more about UQ policies on my.UQ and the Policy and Procedure Library.