Course overview
- Study period
- Semester 2, 2025 (28/07/2025 - 22/11/2025)
- Study level
- Undergraduate
- Location
- St Lucia
- Attendance mode
- In Person
- Units
- 2
- Administrative campus
- St Lucia
- Coordinating unit
- Chemistry & Molec Biosciences
This course covers the principles of microbial genomics and its application to cultured and uncultured microbial diversity (metagenomics), including the use of informational macromolecules such as 16S rRNA. The course emphasises the use of genomics and metagenomics to advance the fields of metabolic engineering, geobiology and human health. This course has content relevant to Biotechnology, Microbiology and Genetics majors.
MICR3004 focuses on microbial genomics including sequencing, assembly, annotation and metabolic reconstruction; microbial diversity; evolution and classification; culture-independent molecular analysis of microbial communities via metagenomics; application of genomics and metagenomics in environmental, engineered and clinical habitats including the human gut, wastewater treatment, and acid mine drainage; biofuels and bioremediation; and host-microbe interactions affecting health and disease.
Course requirements
Assumed background
General microbial science with a focus on molecular biology, environmental and process microbiology and microbial physiology.
Prerequisites
You'll need to complete the following courses before enrolling in this one:
(MICR2000 or MICR2900)
Recommended prerequisites
We recommend completing the following courses before enrolling in this one:
[BIOC2000 or BIOC2900] or [BIOL2202 or BIOL2902]
Course contact
Course staff
Lecturer
Guest lecturer
Dr Laura Rix
Timetable
The timetable for this course is available on the UQ Public Timetable.
Additional timetable information
Check your online timetable regularly.
Aims and outcomes
The aim of MICR3004 is to introduce students to the major concepts in microbial genomics and metagenomics, and how these fields have impacted on our understanding of microbial evolution, physiology and ecology. Through a series of lecture and practical laboratory examples, students will learn how microbial genomics and metagenomics approaches have been applied to understand and manipulate microbial functionality in diverse ecosystems, as well as to isolate "new" microbes from Nature. Such applications will include use and modification of microbial enzymes, methods for diagnosis of microbial diseases, the use of microbes in nanotechnology, the application of microbial physiology and diversity to understanding the treatment of wastewater, and the discovery of drugs such as antibiotics and anti-cancer compounds via exploitation of microbial diversity and understanding of the microbial genome.
Learning outcomes
After successfully completing this course you should be able to:
LO1.
demonstrate awareness of and illustrate the depth and breadth of the field of microbial genomics
LO2.
link fundamental knowledge of microbial ecosystems with applied real-world applications
LO3.
examine the potential of microbial genomics and metagenomics in microbial biodiversity measurement and biotechnology
LO4.
establish an understanding of key microbial biotechnology research techniques, via practical laboratory experience
LO5.
conduct a literature review and perform a critical analysis of metagenomic data
LO6.
examine how culture-independent molecular methods are used to assess the diversity of natural microbial communities
LO7.
understand the nature of microbial biofilms, and their implications, both positive and negative
LO8.
evaluate microbial contributions to environmental sustainability and remediation
Assessment
Assessment summary
| Category | Assessment task | Weight | Due date |
|---|---|---|---|
| Notebook/ Logbook |
Laboratory Notebooks
|
5% |
6/08/2025 - 10/09/2025 |
| Presentation |
Methods Oral Presentation
|
15% |
17/09/2025 2:00 pm |
| Paper/ Report/ Annotation | Bioleaching Microbiome Report | 30% |
29/10/2025 2:00 pm |
| Examination |
End of Semester Exam
|
50% |
End of Semester Exam Period 8/11/2025 - 22/11/2025 |
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
Laboratory Notebooks
- Identity Verified
- In-person
- Mode
- Written
- Category
- Notebook/ Logbook
- Weight
- 5%
- Due date
6/08/2025 - 10/09/2025
- Learning outcomes
- L04
Task description
Participation in lab practical and record keeping of lab notebook including answering pre-set questions at the end of each practical: 1% per week for the first five practicals (i.e. the molecular biology component). Laboratory notebooks will be marked in class by your tutor.
Use of Artificial Intelligence (AI) and Machine Translation (MT)
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.
Submission guidelines
Lab notebooks and questions will be marked in class at the beginning of the following week.
Deferral or extension
You cannot defer or apply for an extension for this assessment.
If you miss a practical due to illness (with medical certificate), your marks for the other weeks will be averaged to provide a final mark out of 5%
Late submission
You will receive a mark of 0 if this assessment is submitted late.
You are required to show your lab notebooks to your tutor from week 2 in order to obtain your mark for the previous week. If you do not do this, you will lose your mark for that week.
Methods Oral Presentation
- Identity Verified
- In-person
- Mode
- Oral
- Category
- Presentation
- Weight
- 15%
- Due date
17/09/2025 2:00 pm
- Learning outcomes
- L05
Task description
Students will be assessed on a PowerPoint presentation on a selected topic related to methods learned in the laboratory module.
The ability to communicate effectively is a skill that is valuable not only in a career in Genomics, but in most fields.
Use of Artificial Intelligence (AI) and Machine Translation (MT)
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
Presentations will occur in class and be marked on the day by your tutor.
Deferral or extension
You may be able to apply for an extension.
Applications for extension
Extension applications must be received no later than 24 hours after the published assessment due date and time.
Read the information contained in the following links carefully before submitting an application for extension to assessment due date.
For guidance on applying for an extension, information is available here.
For the policy relating to extensions, information is available here (Part D).
Information on medical certificates
Please note the University's requirements for medical certificates here.
Bioleaching Microbiome Report
- Mode
- Written
- Category
- Paper/ Report/ Annotation
- Weight
- 30%
- Due date
29/10/2025 2:00 pm
- Learning outcomes
- L01, L02, L03, L05, L06, L07, L08
Task description
The findings of the 10 week laboratory course are to be summarised in a report following the format of the journal Genome Research.
Use of Artificial Intelligence (AI) and Machine Translation (MT)
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
Submit your assessment item through the course Turnitin submission point in Blackboard. Before submitting your assessment item to Turnitin please name your file in the following way. FAMILY NAME_GivenName_StudentID_CourseCode_AssignmentName For example: Bob Smith (ID: 54329876) would name his ABCD1234 essay 1 in the following way. SMITH_Bob_54329876_ABCD1234_Essay1
Deferral or extension
You may be able to apply for an extension.
Applications for extension
Extension applications must be received no later than 24 hours after the published assessment due date and time.
Read the information contained in the following links carefully before submitting an application for extension to assessment due date.
For guidance on applying for an extension, information is available here.
For the policy relating to extensions, information is available here (Part D).
Information on medical certificates
Please note the University's requirements for medical certificates here.
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.
You are required to submit assessable items on time. If you fail to meet the submission deadline for any assessment item, then 10% of the maximum possible mark for the assessment item (assessment ‘marked from’ value) will be deducted as a late penalty for every day (or part day) late after the due date. For example, if you submit your assignment 1 hour late, you will be penalised 10%; if your assignment is 24.5 hours late, you will be penalised 20% (because it is late by one 24-hour period plus part of another 24-hour period). 10% will be deducted per day for up to 7 calendar days, at which point your submission will receive a mark of zero (0) unless an extension has been approved.
In most instances one or more hurdles will apply to your assessment item so you will need to submit it to fulfil the requirements of the course regardless of how late it is and the mark you are likely to be awarded.
End of Semester Exam
- Hurdle
- Identity Verified
- In-person
- Mode
- Written
- Category
- Examination
- Weight
- 50%
- Due date
End of Semester Exam Period
8/11/2025 - 22/11/2025
- Learning outcomes
- L01, L02, L03, L06, L07, L08
Task description
The examination samples knowledge from the course lectures. More information will be provided in person and on Blackboard.
Use of Artificial Intelligence (AI) and Machine Translation (MT)
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
See ADDITIONAL COURSE GRADING INFORMATION for the hurdle/s relating to this assessment item.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: Work not submitted or examinations answered with blank pages or complete lack of demonstration of any knowledge of lecture or practical material. The minimum percentage required for this grade is: 0% |
| 2 (Fail) |
Minimal evidence of achievement of course learning outcomes. Course grade description: Work of very poor quality, very little understanding of subject matter. The minimum percentage required for this grade is: 30% |
| 3 (Marginal Fail) |
Demonstrated evidence of developing achievement of course learning outcomes Course grade description: Falls short of satisfying all basic requirements for a pass. The minimum percentage required for this grade is: 45% |
| 4 (Pass) |
Demonstrated evidence of functional achievement of course learning outcomes. Course grade description: Work of fair quality, demonstrating a basic understanding of most aspects of subject matter and a modest appreciation of issues covered in lectures and practical components, but serious deficiencies in some areas. The minimum percentage required for this grade is: 50% |
| 5 (Credit) |
Demonstrated evidence of proficient achievement of course learning outcomes. Course grade description: Work of good quality, demonstrating a good understanding of most subject matter but with some inadequacies. The minimum percentage required for this grade is: 65% |
| 6 (Distinction) |
Demonstrated evidence of advanced achievement of course learning outcomes. Course grade description: Work of very good quality, demonstrating a strong understanding of subject matter. The minimum percentage required for this grade is: 75% |
| 7 (High Distinction) |
Demonstrated evidence of exceptional achievement of course learning outcomes. Course grade description: Work of exceptional quality, demonstrating deep understanding of the subject matter. The minimum percentage required for this grade is: 85% |
Additional course grading information
Assessment Hurdles
In order to pass this course, you must meet ALL of the following requirements (if you do not meet these requirements, the maximum grade you will receive will be a 3):
1. You must obtain an overall mark of 40% or more on the end of semester exam
2. You must complete 100% of the laboratory component of the course.
Supplementary assessment
Supplementary assessment is available for this course.
Should you fail a course with a grade of 3, you may be eligible for supplementary assessment. Refer to my.UQ for information on supplementary assessment and how to apply.
Supplementary assessment provides an additional opportunity to demonstrate you have achieved all the required learning outcomes for a course.
If you apply and are granted supplementary assessment, the type of supplementary assessment set will consider which learning outcome(s) have not been met.
Supplementary assessment can take any form (such as a written report, oral presentation, examination or other appropriate assessment) and may test specific learning outcomes tailored to the individual student, or all learning outcomes.
To receive a passing grade of 3S4, you must obtain a mark of 50% or more on the supplementary assessment.
Additional assessment information
Assessment Submission
It is the responsibility of the student to ensure the on time, correct and complete submission of all assessment items.
Students are responsible for retaining evidence of submission by the due date for all assessment items, in the required form (for example, screenshot, email, photo, and an unaltered copy of submitted work).
In the case of a Blackboard outage, contact the Course Coordinator as soon as possible to confirm the outage with ITS.
Assessment/Attendance
Notify your Course Coordinator as soon as you become aware of any issue that may affect your ability to meet the assessment/attendance requirements of the course. The my.UQ website and the Course Profile (CP) for your course provide information about your course requirements, the rules associated with your courses and services offered by the University.
A note for repeating students in this course
Only learning activities and/or assessment items completed during the study period of enrolment, including any approved extensions, may contribute to your grade in this course. The whole or partial use of assessment items previously submitted for the same course, for a course at any institution, or for published material, is not permitted without written permission of the Course Coordinator.
Important Note
Turnitin is to be used for assignments/laboratory reports to check for plagiarism. Penalties can be severe for plagiarism.
The University has adopted the following definition of plagiarism: Plagiarism is the act of misrepresenting as one's own original work the ideas, interpretations, words or creative works of another either intentionally or unintentionally. These include published and unpublished documents, designs, music, sounds, images, photographs, computer codes and ideas gained through working in a group. These ideas, interpretations, words or works may be found in print and/or electronic media.
Students should read the UQ Student Integrity and Misconduct Policy.
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
Library resources are available on the UQ Library website.
Additional learning resources information
Lecturers will provide students with information on access to source literature and relevant web sites.
Blackboard
Additional material (including the Turnitin portal) may be found on the Blackboard site for MICR3004 at learn.uq.edu.au
Check the Announcements section of the Blackboard site regularly for information updates.
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 2 |
Lecture |
Microbial genomics from an evolutionary perspective A series of six lectures introducing microbial genomics and culture-independent sequence-based exploration of microbial diversity by Phil Hugenholtz Learning outcomes: L01, L02, L03, L06, L08 |
Multiple weeks From Week 1 To Week 6 |
Practical |
Molecular biology practical A 5 week laboratory practical characterising the microbiomes of bioleaching columns including measurement of column parameters, extracting DNA from bioleaching column samples, PCR-amplification of 16S rRNA genes, creating metagenomic sequencing libraries and imaging microbial cells using fluorecence in sity hybridisation (FISH) Learning outcomes: L01, L04 |
Multiple weeks From Week 4 To Week 5 |
Lecture |
Microbial genomics from a metabolic perspective A series of six lectures covering metabolic reconstruction of genome sequences and metabolic engineering by Ulrike Kappler Learning outcomes: L01, L03 |
Multiple weeks From Week 6 To Week 7 |
Lecture |
Guest Lecture on marine ecosystems Three guest lectures on Microbial genomics in marine ecosystems by Laura Rix Learning outcomes: L01, L02, L06 |
Multiple weeks From Week 7 To Week 11 |
Practical |
Bioinformatics practical A 5 week bioinformatics practical covering taxonomic and functional profiling of bioleaching column microbial communities from a gene- and genome-centric viewpoint Learning outcomes: L01, L03, L05, L06, L08 |
Multiple weeks From Week 8 To Week 9 |
Lecture |
Microbial genomics in clinical ecosystems A series of six lectures exploring the human microbiome in health and disease by Marloes Nitert Dekker Learning outcomes: L01, L02, L07 |
Multiple weeks From Week 10 To Week 13 |
Lecture |
Microbial genomics in engineered and environmental ecosystems A series of six lectures on biofilms, bioremediation and biogeochemistry from a microbial perspective by Gordon Southam Learning outcomes: L01, L02, L03, L07, L08 |
Additional learning activity information
Week 12 - Wednesday 22nd October, 2pm, will be available for a "drop-in" session for students who have assignment questions.
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 for Students Policy and Procedure
Learn more about UQ policies on my.UQ and the Policy and Procedure Library.
You'll also need to be aware of the following policies and procedures while completing this course:
- Laboratory Occupational Health and Safety