Microbial Genomics (MICR3004)

Course overview

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

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:

Assessment

Assessment summary

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

• Hurdle
• Identity Verified
• In-person

Mode

Written

Category

Notebook/ Logbook

Weight

5%

Due date

31/07/2024 - 4/09/2024

Learning outcomes

L04

Task description

Hurdle requirements

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

• Hurdle
• Identity Verified
• In-person

Mode

Oral

Category

Presentation

Weight

15%

Due date

11/09/2024 2:00 pm

Learning outcomes

L05

Task description

Hurdle requirements

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 Extensions

Information on applying for an extension can be found here: my.UQ Applying for an extension.

Extension applications must be received by the assessment due date and time.

If you are unable to provide approved documentation to support your application by the due date and time, you must still submit your application by the deadline but with an attached Word document that outlines why you cannot provide the approved documentation by the deadline. You will then need to acquire and upload the approved documentation to your request within 24 hours. Please note: When an extension request has been submitted and is pending, students are expected to continue to work on the assessment item, with the aim of submitting by the requested due date and time.

Prolonged Absence

If you have been ill or unable to attend class for more than 14 days, we advise you to carefully consider whether you are capable of successfully completing your courses this semester.

Extensions with Student Access Plans (SAP)

For extensions up to 7 days, your SAP is all that is required as documentation to support your application. However, extension requests longer than 7 days (for any one assessment item) will require the submission of additional supporting documentation e.g. a medical certificate.

Bioleaching Microbiome Report

• Hurdle

Mode

Written

Category

Paper/ Report/ Annotation

Weight

30%

Due date

23/10/2024 2:00 pm

Learning outcomes

L01, L02, L03, L05, L06, L07, L08

Task description

Hurdle requirements

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 Extensions

Information on applying for an extension can be found here: my.UQ Applying for an extension.

Extension applications must be received by the assessment due date and time.

If you are unable to provide approved documentation to support your application by the due date and time, you must still submit your application by the deadline but with an attached Word document that outlines why you cannot provide the approved documentation by the deadline. You will then need to acquire and upload the approved documentation to your request within 24 hours. Please note: When an extension request has been submitted and is pending, students are expected to continue to work on the assessment item, with the aim of submitting by the requested due date and time.

Prolonged Absence

If you have been ill or unable to attend class for more than 14 days, we advise you to carefully consider whether you are capable of successfully completing your courses this semester.

Extensions with Student Access Plans (SAP)

For extensions up to 7 days, your SAP is all that is required as documentation to support your application. However, extension requests longer than 7 days (for any one assessment item) will require the submission of additional supporting documentation e.g. a medical certificate.

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

2/11/2024 - 16/11/2024

Learning outcomes

L01, L02, L03, L06, L07, L08

Task description

Hurdle requirements

Exam details

Submission guidelines

Deferral or extension

You may be able to defer this exam.

Applications for Extensions

Information on applying for an extension can be found here: my.UQ Applying for an extension.

Extension applications must be received by the assessment due date and time.

A maximum of two applications may be submitted for any one assessment item, unless exceptional circumstances can be demonstrated. If you are unable to provide approved documentation to support your application by the due date and time, you must still submit your application by the deadline but with an attached Word document that outlines why you cannot provide the approved documentation by the deadline. You will then need to acquire and upload the approved documentation to your request within 24 hours. Please note: When an extension request has been submitted and is pending, students are expected to continue to work on the assessment item, with the aim of submitting by the requested due date and time.

Prolonged Absence

If you have been ill or unable to attend class for more than 14 days, we advise you to carefully consider whether you are capable of successfully completing your courses this semester.

Extensions with Student Access Plans (SAP)

For extensions up to 7 days, your SAP is all that is required as documentation to support your application. However, extension requests longer than 7 days (for any one assessment item) will require the submission of additional supporting documentation e.g. a medical certificate.

Course grading

Full criteria for each grade is available in the Assessment Procedure.

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 50% or more; and

2.  You must obtain an overall mark of 40% or more in the end of semester exam; and

3.  You must obtain a minimum weighted average mark of 40% across all other non-examination course assessment items and learning tasks; and

4. You must attend 100% of the practical component of the course and complete and submit ALL practical assessment.

The maximum grade you will receive will be a 2 if you:

1. Obtain an overall mark of 30% or less on the end of semester exam; and/or

2. Obtain a weighted average mark of 30% or less on the non-examination course assessment items and learning tasks.

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.

Please ensure you receive and save the submission confirmation for all submitted items, you may be asked to produce this as evidence of your submission.

Turnitin

By submitting work through Turnitin you are deemed to have accepted the following declaration “I certify that this assignment is my own work and has not been submitted, either previously or concurrently, in whole or in part, to this University or any other educational institution, for marking or assessment”.

All students must ensure they receive their Turnitin receipt on submission of any assessments. A valid Turnitin receipt will be the only evidence accepted if one or more of your submissions are missing. Without evidence, the assessment will receive the standard late penalty, or after seven days, will receive zero. In the case of a Blackboard outage, please contact the Course Coordinator as soon as possible to confirm the outage with ITS.

Assessment/Attendance

Please 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 Electronic Course Profile (ECP) for your course also 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

Any student who enrols in a course must not be given exemption or partial credit from their previous attempt(s) for any individual piece of assessment. Instead, the student must successfully complete all of the learning activities and assessment items within the study period of enrolment (PPL Assessment - Procedures Section: Assessment integrity).

If the same assessment item is set from one year to the next, repeating students are allowed to submit the same work they submitted in previous attempts at the course. Where possible SCMB recommends that you use the feedback you received in your last attempt to improve parts of the item where you lost marks. Resubmission of an altered or unaltered assessment item by a repeating student (where the same assessment has been set) will not be considered as self-plagiarism.

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 are encouraged to read the UQ Academic Integrity and Plagiarism 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

Find the required and recommended resources for this course 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.

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.

You'll also need to be aware of the following policies and procedures while completing this course:

• Laboratory Occupational Health and Safety