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BIO3051 : Microbial Genomics

  • Offered for Year: 2020/21
  • Module Leader(s): Dr Maria Del Carmen Montero-Calasanz
  • Lecturer: Dr Jon Marles-Wright, Dr James Stach
  • Owning School: Natural and Environmental Sciences
  • Teaching Location: Newcastle City Campus
Semester 2 Credit Value: 20
ECTS Credits: 10.0


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
•       Evolutionary and comparative 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

Module leaders are revising this content in light of the Covid 19 restrictions.
Revised and approved detail information will be available by 17 August.

Assessment Methods

Module leaders are revising this content in light of the Covid 19 restrictions.
Revised and approved detail information will be available by 17 August.

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