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NES3307 : Microbial Genomics

  • Offered for Year: 2023/24
  • Module Leader(s): Dr James Stach
  • Lecturer: Dr Jon Marles-Wright
  • Owning School: Natural and Environmental Sciences
  • Teaching Location: Newcastle City Campus

Your programme is made up of credits, the total differs on programme to programme.

Semester 2 Credit Value: 20
ECTS Credits: 10.0
European Credit Transfer System


The module primarily aims to develop students' knowledge and hands-on experience in prokaryotic genomic science, enriching their understanding of microbial metabolism, diversity, structure, evolution, and the potential of microbes as natural resource. It aspires to contribute to their development as independent researchers and to introduce the interdisciplinary nature of biological research.
Knowledge-based aims include key discoveries in genomic science; sequencing techniques, concepts and applications; and recognition and interpretation of connections between genotype and phenotype.
Skills-based aims include development of laboratory skills in microbiology, molecular biology and high-throughput DNA sequencing technologies (Oxford Nanopore technology); and bioinformatics skills in quality control, assembly, annotation, mining and phylogenomic inference of bacterial genome and metagenomic datasets;

Outline Of Syllabus

This is a student-led research module that combines practical learning through student-directed laboratory (wet and dry sessions) and inquiry-based learning in which posing questions, problems and scenarios related to genomic science are introduced by a facilitator and inquirers identify and research issues and questions to develop knowledge, or solutions.
The module consists of a series of workshops (including computer-based workshops) and student-driven practical sessions addressing two broad challenges: microbial diversity and functional genomics. An introductory workshop provide students with an overview to the concepts of student-led research and flipped learning. Students are then provided with information about the research goal i.e. genome sequencing and functional mining of bacterial plant endophytes. They are provided with details about the origin and preliminary data of provided endophytes and examples of biotechnological applications that rely on plant endophytes as well as insights into their ecology and metabolism. In the following workshops, students are introduced to sequencing technologies and hypothesis generation and experimental design in the field of genomics; and are encouraged to prepare and discuss their own research plans. After making a decision on their research direction, student-driven practical sessions in DNA extraction and purification, DNA library preparation and DNA sequencing are provided. Following those, students are provided with practical knowledge in genomic analysis and interpretation through workshops covering the topics:

•       Introduction to command line
•       Assembly and annotation of sequences
•       Genomic mining
•       Functional genomics
•       Metagenomics
•       Scientific writing –Genomic papers

All the workshops follow a flipped-classroom, active-learning model, with students working on the learning resources provided on Blackboard in their non-contact time (prior and after sessions) and on problem-solving and peer-discussion during the sessions. Those are designed to enable students to become familiar with the basic tools used for genomics and to develop their independent learning skills, teamwork and critical thinking. Ongoing formative feedback through dialogue with the academic facilitator is provided in each workshop and during practical sessions.

Teaching Methods

Teaching Activities
Category Activity Number Length Student Hours Comment
Guided Independent StudyAssessment preparation and completion18:008:00Research project plan preparation
Guided Independent StudyAssessment preparation and completion155:0055:00Research Paper
Guided Independent StudyAssessment preparation and completion125:0025:00Practical/Lab report
Guided Independent StudyDirected research and reading185:0090:00Read and work on material prior and after workshops
Scheduled Learning And Teaching ActivitiesPractical23:006:00PiP - Students will be present in the laboratory for practical sessions
Scheduled Learning And Teaching ActivitiesWorkshops161:0016:00Topic introduction and problem-solving exercises (mostly computer lab sessions)
Teaching Rationale And Relationship

This module is designed to provide a pedagogical opportunity integrating hands-on research and core scientific competencies (i.e. experimental design, hypothesis generation, laboratory skills) with emerging next generation sequencing technologies to strengthen UG experiences in STEM education and contribute to their development as independent researchers.

Workshops based on problem-solving activities provide knowledge and help students develop awareness of key aspects of genomic science and critical analysis. Computer-based workshops gives students hands-on experience in analysing and genomic data interpretation.

Genomics is a rapidly evolving field – students are encouraged to read key papers from discovery and review journals to keep abreast of developments and to develop a critical appreciation of genomic science, its strengths and limitations. Private study prior sessions is therefore essential for students to fully understand and absorb material covered in workshops and to become familiar with genomic concepts, technologies and bioinformatics tools used for genome analysis and interpretation.

Assessment Methods

The format of resits will be determined by the Board of Examiners

Other Assessment
Description Semester When Set Percentage Comment
Practical/lab report2M30N/A
Research paper2M703000 words
Formative Assessments

Formative Assessment is an assessment which develops your skills in being assessed, allows for you to receive feedback, and prepares you for being assessed. However, it does not count to your final mark.

Description Semester When Set Comment
Computer assessment2MCovid-19 genome assembly and annotation. Student work through a series of online tutorials and task sheets that trains then show to assembly sequencing data, search their assembly for protein-coding regions, annotate these regions and compare their assembly with reference genomes.
Assessment Rationale And Relationship

Summative assessments aim to assess different aspects of knowledge, understanding and integration of subject material obtained from workshops and practical sessions.
The research paper assess dry professional skills in sequencing and analysis of a bacterial genome and students' ability to interpret genomic data, in terms of technical limitations, genotype-phenotype correlations, evolutionary processes and potential biotechnological uses.
The practical/lab report assess general dry professional skills and students’ understanding in sequencing, assembly and annotation of a given genomic dataset.
Assessment lengths and required workload has been chosen to allow the students sufficient scope to explore and express the technical detail and the academic depth of the topics associated with the subject at this level and therefore to ensure they cover all learning outcomes associated.
Formative assessment and feedback are provided during sessions.

Reading Lists