The course will describe how ecological factors play an important role in animal health.  For example the gain and loss of strains from a host, within host population dynamics, e.g. competition, and among host dynamics, e.g. transmission.  Transmission will be examined in the light of many recent studies looking at how social networks are important determinants of disease transmission in a population.  Many of these questions will be addressed looking at individual bacterial species and a variety of hosts, both human and animal.

The course will also look at the animal microbial communities, and their role in nutrition, disease prevention, and as a cause of disease.  The course would include topics related to the diversity of host associated microbial communities, including the factors affecting the composition and stability of these communities.

The course will include a significant section on the evolution of bacterial genomes and accessory elements, in particular the evolution of virulence and bacterial adaptation.  The course would emphasise the fact that bacteria evolve in ‘real time’ as it were and that new pathogens are continually emerging.  For example, the newly evolved E. coli intestinal pathogen that caused disease outbreaks in Europe.

 

Learning Outcomes

Upon successful completion, students will have the knowledge and skills to:

On satisfying the requirements of this course, student will have the knowledge and skills to:

1. Investigate the processes responsible for shaping the clonal composition of a bacterial species as well as the bacterial community composition within a host.
2. Critically evaluate how the human gut microbiota influences human health.
3. Critically evaluate how spatial relationships and social interactions determine bacterial transmission among hosts.
4. Investigate and analyse quantitatively the processes that underlie bacterial genome evolution.
5. Apply a range of bioinformatics techniques used in comparative genomics.
6. Employ high order laboratory techniques.

Examination Material or equipment

No permitted materials

Required Resources

Students will need access to a computer which can be a personally owned device or via the computer labs.

Staff Feedback

Students will be given feedback in the following forms in this course:

• written comments
• verbal comments
• feedback to whole class, groups, individuals, focus group etc

Student Feedback

ANU is committed to the demonstration of educational excellence and regularly seeks feedback from students. Students are encouraged to offer feedback directly to their Course Convener or through their College and Course representatives (if applicable). The feedback given in these surveys is anonymous and provides the Colleges, University Education Committee and Academic Board with opportunities to recognise excellent teaching, and opportunities for improvement. The Surveys and Evaluation website provides more information on student surveys at ANU and reports on the feedback provided on ANU courses.

Class Schedule

Week/Session	Summary of Activities	Assessment
1	Course Introduction Bacterial strain typing	No practical
2	Bacterial strain typing Introduction to practical	Compulsory practical
3	Bacterial genome evolution	Compulsory practical
4	Bioinformatic methods E.coli population genetics	Compulsory practical
5	E. coli population genetics	Compulsory practical
6	E. coli and extra-intestinal infection Bioinformatic methods	Compulsory practical Presentation of assignment expectations
7	Mid semester break
8	Mid semester break
9	Food as a source of E. coli pathogens Bioinformatic methods	Assignment One due
10	Microbial community analysis Background and expectations for Assignment Two	Attendance at lecture presenting Assignment Two is compulsory
11	Microbial community analysis Bioinformatic methods
12	Gut microbiome and health
13	Evolution at the gene level
14	No lectures - Work on Assignment Two	Assignment Two due

Assessment Summary

Assessment task	Value	Due Date	Return of assessment	Learning Outcomes
Assignment One	20 %	16/09/2019	30/09/2019	5,6
Assignment Two	50 %	25/10/2019	15/11/2019	4,5
Final Exam	30 %	31/10/2019	28/11/2019	1,2,3,4

* If the Due Date and Return of Assessment date are blank, see the Assessment Tab for specific Assessment Task details

Policies

ANU has educational policies, procedures and guidelines, which are designed to ensure that staff and students are aware of the University’s academic standards, and implement them. Students are expected to have read the Academic Misconduct Rule before the commencement of their course. Other key policies and guidelines include:

• Student Assessment (Coursework) Policy and Procedure
• Special Assessment Consideration Policy and General Information 
• Student Surveys and Evaluations
• Deferred Examinations
• Student Complaint Resolution Policy and Procedure

Assessment Requirements

The ANU is using Turnitin to enhance student citation and referencing techniques, and to assess assignment submissions as a component of the University's approach to managing Academic Integrity. For additional information regarding Turnitin please visit the ANU Online website. In rare cases where online submission using Turnitin software is not technically possible; or where not using Turnitin software has been justified by the Course Convener and approved by the Associate Dean (Education) on the basis of the teaching model being employed; students shall submit assessment online via ‘Wattle’ outside of Turnitin, or failing that in hard copy, or through a combination of submission methods as approved by the Associate Dean (Education). The submission method is detailed below.

Moderation of Assessment

Marks that are allocated during Semester are to be considered provisional until formalised by the College examiners meeting at the end of each Semester. If appropriate, some moderation of marks might be applied prior to final results being released.

Participation

There are 5 practical sessions scheduled in August and attendance of each practical for the entire practical is compulsory

Examination(s)

The final exam will be held during the exam period. The date range in the Assessment Summary indicates the start of the end of semester exam period and the date official end of semester results are released on ISIS. Please check the ANU final Examination Timetable http://www.anu.edu.au/students/program-administration/assessments-exams/examination-timetable to confirm the date, time and location exam.

Assessment Task 1

Assignment One

Write up in the form of a scientific paper the results of practical work undertaken as part of this course.

Assessment Task 2

Assignment Two

Analyse using a variety of bioinformatic techniques and web-based resources whole genome sequence data to address a set of specific questions relevant to the ecology and evolution of Escherichia coli. You will receive comments on ONE draft of your Assignment Two provided that 1) It is a complete draft (excluding reference list). 2) The draft is submitted (via email to the course convenor) by 5:00 pm November 21.

Assessment Task 3

Final Exam

Answer a series of short answer questions covering the material presented during lectures.

Previous exams are not available online, but you will be provided with sample exam questions prior to end of term

Academic Integrity

Academic integrity is a core part of the ANU culture as a community of scholars. At its heart, academic integrity is about behaving ethically, committing to honest and responsible scholarly practice and upholding these values with respect and fairness.

The ANU commits to assisting all members of our community to understand how to engage in academic work in ways that are consistent with, and actively support academic integrity. The ANU expects staff and students to be familiar with the academic integrity principle and Academic Misconduct Rule, uphold high standards of academic integrity and act ethically and honestly, to ensure the quality and value of the qualification that you will graduate with.

The Academic Misconduct Rule is in place to promote academic integrity and manage academic misconduct. Very minor breaches of the academic integrity principle may result in a reduction of marks of up to 10% of the total marks available for the assessment. The ANU offers a number of online and in person services to assist students with their assignments, examinations, and other learning activities. Visit the Academic Skills website for more information about academic integrity, your responsibilities and for assistance with your assignments, writing skills and study.

Online Submission

You will be required to electronically sign a declaration as part of the submission of your assignment. Please keep a copy of the assignment for your records. Unless an exemption has been approved by the Associate Dean (Education) submission must be through Turnitin.

Hardcopy Submission

For some forms of assessment (hand written assignments, art works, laboratory notes, etc.) hard copy submission is appropriate when approved by the Associate Dean (Education). Hard copy submissions must utilise the Assignment Cover Sheet. Please keep a copy of tasks completed for your records.

Late Submission

Individual assessment tasks may or may not allow for late submission. Policy regarding late submission is detailed below:

• Late submission permitted. Late submission of assessment tasks without an extension are penalised at the rate of 5% of the possible marks available per working day or part thereof. Late submission of assessment tasks is not accepted after 10 working days after the due date, or on or after the date specified in the course outline for the return of the assessment item. Late submission is not accepted for take-home examinations.

Referencing Requirements

Accepted academic practice for referencing sources that you use in presentations can be found via the links on the Wattle site, under the file named “ANU and College Policies, Program Information, Student Support Services and Assessment”. Alternatively, you can seek help through the Students Learning Development website.

Extensions and Penalties

Extensions and late submission of assessment pieces are covered by the Student Assessment (Coursework) Policy and Procedure. The Course Convener may grant extensions for assessment pieces that are not examinations or take-home examinations. If you need an extension, you must request an extension in writing on or before the due date. If you have documented and appropriate medical evidence that demonstrates you were not able to request an extension on or before the due date, you may be able to request it after the due date.

Resubmission of Assignments

Not permitted

Privacy Notice

The ANU has made a number of third party, online, databases available for students to use. Use of each online database is conditional on student end users first agreeing to the database licensor’s terms of service and/or privacy policy. Students should read these carefully. In some cases student end users will be required to register an account with the database licensor and submit personal information, including their: first name; last name; ANU email address; and other information.
In cases where student end users are asked to submit ‘content’ to a database, such as an assignment or short answers, the database licensor may only use the student’s ‘content’ in accordance with the terms of service – including any (copyright) licence the student grants to the database licensor. Any personal information or content a student submits may be stored by the licensor, potentially offshore, and will be used to process the database service in accordance with the licensors terms of service and/or privacy policy.
If any student chooses not to agree to the database licensor’s terms of service or privacy policy, the student will not be able to access and use the database. In these circumstances students should contact their lecturer to enquire about alternative arrangements that are available.

Distribution of grades policy

Academic Quality Assurance Committee monitors the performance of students, including attrition, further study and employment rates and grade distribution, and College reports on quality assurance processes for assessment activities, including alignment with national and international disciplinary and interdisciplinary standards, as well as qualification type learning outcomes.

Since first semester 1994, ANU uses a grading scale for all courses. This grading scale is used by all academic areas of the University.

Support for students

The University offers students support through several different services. You may contact the services listed below directly or seek advice from your Course Convener, Student Administrators, or your College and Course representatives (if applicable).

• ANU Health, safety & wellbeing for medical services, counselling, mental health and spiritual support
• ANU Diversity and inclusion for students with a disability or ongoing or chronic illness
• ANU Dean of Students for confidential, impartial advice and help to resolve problems between students and the academic or administrative areas of the University
• ANU Academic Skills and Learning Centre supports you make your own decisions about how you learn and manage your workload.
• ANU Counselling Centre promotes, supports and enhances mental health and wellbeing within the University student community.
• ANUSA supports and represents undergraduate and ANU College students
• PARSA supports and represents postgraduate and research students