BI1FM1: Fundamentals of Microbiology

Module code: BI1FM1

Module provider: School of Biological Sciences

Credits: 20

Level: 4

When you'll be taught: Semester 1

Module convenor: Dr Geraldine Mulley, email: g.mulley@reading.ac.uk

Module co-convenor: Dr Glyn Barrett, email: glyn.barrett@reading.ac.uk

Pre-requisite module(s):

Co-requisite module(s):

Pre-requisite or Co-requisite module(s):

Module(s) excluded:

Placement information: NA

Academic year: 2024/5

Available to visiting students: Yes

Talis reading list: Yes

Last updated: 11 December 2024

Overview

Module aims and purpose

This module will provide you with a strong foundation in the discipline of Microbiology. You will learn the fundamental biology of bacteria, archaea, protists, fungi and viruses and discover their amazing diversity, exploring microbial structure, genetics, replication, nutrition, ecology and evolution. You will consider why microbes are only able to live in certain environmental conditions, including on or inside other organisms, and how some microbes benefit society whilst others cause harm. You will gain a broad understanding of how pathogens cause infections, the various ways to diagnose, treat and prevent infectious diseases in humans, animals, and plants, and find out how microbes evolve antimicrobial resistance. You will gain insight into the methods used to classify microbes and put some of these techniques into practice in the practical classes to identify bacteria from environmental samples. You will also learn how to safely work with microbiological samples using aseptic technique, and to isolate, purify, stain, and observe microbial cells using the light microscope. You will also be taught how to search for scientific literature on a selected area of microbiology to produce a piece of written work that communicates interesting details and concepts in a scientific style. 

Module learning outcomes

By the end of the module, it is expected that students will be able to:

1. Describe the fundamental characteristics of the 5 major groups of microbes, comparing their structure, genetics, replication, nutrition, ecology, and evolution, and discuss their diversity in relation to the environmental niches they inhabit.
2. Explain how some microbes cause infectious diseases and how they are transmitted, diagnosed, treated, and prevented, including the mechanism of action of antimicrobials and principles of vaccination.
3. Describe key landmarks in microbiology research and discuss the ways in which this can benefit society through applications in medicine, food, environment, and biotechnology.
4. Explain the principles of aseptic technique and core microbiology practical techniques, and use some of these methods to safely isolate, purify and identify microbes from food and environmental samples, keeping an accurate record of observations and results.
5. Search for, integrate and summarise scientific literature to communicate key concepts in microbiology in a scientific writing style, citing relevant literature and compiling a bibliography using the Harvard system.

Module content

Lecture material includes the following topics:

• Prokaryotic microbes: structure and function, replication, growth optima, nutritional strategies and biochemistry of bacteria and archaea
• Eukaryotic microbes: structure and function, replication, growth optima, nutritional strategies and biochemistry of fungi and protists
• Acellular microbes: structure, function and replication of viruses and other acellular entities (satellites, viroids, prions)
• Microbial ecology: concept of niches, free-living, commensals and pathogens, microbial competition and cooperation, host-microbe interactions, microbiomes
• Microbial evolution: origin and diversity of microbes, RNA world hypothesis, LUCA and the tree of life, endosymbiotic theory, mutations, recombination, genetic drift, genetic shift, natural selection, horizontal gene transfer, experimental evolution
• Microbial classification: concept of species, methods for phenetic, molecular and phylogenetic classification, building basic phylogenetic trees, BLAST analysis
• Methods in microbiological research: bacterial growth curves and mean generation times, enumeration of bacteria and viruses, molecular techniques e.g. PCR, serological techniques e.g ELISA, microscopy, bioprospecting for natural products e.g. antibiotics
• Infectious diseases: transmission, diagnosis, treatment, prevention, epidemiology. Selected case studies include human, animal and plant diseases relevant to medicine, veterinary science and agriculture
• Food microbiology: food production (inc. biocontrol, biofertilisers), food spoilage, food preservation, food poisoning and food-borne diseases
• Environmental microbiology: nutrient cycling, climate change, biofuels, bioremediation
• Microbial biotechnology: enzymes for molecular biology, genetic engineering (inc. CRISPR/cas), recombinant protein production in E. coli, yeast and baculoviruses

Practical classes include the following training / activities:

• Good microbiological practice (GMP) including aseptic technique
• Isolation and enumeration of bacteria and bacteriophages from samples (inc. food, lake/river water and soil) using streak plate, pour plate, spread plate and plaque assay techniques
• Culture of bacteria and fungi in solid and liquid media, including selective and differential
• Purification of a single species from a mixed culture
• Gram stain and observation of bacteria and fungi using light microscope with x100 oil immersion lens, inc. measurement of cell dimensions
• Identification of bacteria to the genus / species level using phenetic and molecular techniques
• Bioprospecting for antibiotic producing soil bacteria

Tutorials include the following training / activities:

• Accurate record keeping and basic data handling
• Interpretation of practical results, including calculation of titres and mean generation times
• Scientific writing, academic integrity and referencing including use of reference manager software

Structure

Teaching and learning methods

The learning outcomes will be met through a mixture of lectures, tutorials, laboratory-based practical classes, self-directed learning and directed independent study, which includes completion of an online course designed specifically for this module. Appropriate supplementary information and reading lists will be provided on Blackboard.

Tutorial sessions will prepare and support students to write a scientific essay, including scientific writing, referencing and time management. They will also provide training on how to make accurate records of experimental work and to perform calculations required for the practical assessments.

Study hours

At least 40 hours of scheduled teaching and learning activities will be delivered in person, with the remaining hours for scheduled and self-scheduled teaching and learning activities delivered either in person or online. You will receive further details about how these hours will be delivered before the start of the module.

Please note the independent study hours above are notional numbers of hours; each student will approach studying in different ways. We would advise you to reflect on your learning and the number of hours you are allocating to these tasks.

Semester 1 The hours in this column may include hours during the Christmas holiday period.

Semester 2 The hours in this column may include hours during the Easter holiday period.

Summer The hours in this column will take place during the summer holidays and may be at the start and/or end of the module.

Assessment

Requirements for a pass

Students need to achieve an overall module mark of 40% to pass this module.

Summative assessment

Penalties for late submission of summative assessment

The Support Centres will apply the following penalties for work submitted late:

Assessments with numerical marks

• where the piece of work is submitted after the original deadline (or any formally agreed extension to the deadline): 10% of the total marks available for that piece of work will be deducted from the mark for each working day (or part thereof) following the deadline up to a total of three working days;
• the mark awarded due to the imposition of the penalty shall not fall below the threshold pass mark, namely 40% in the case of modules at Levels 4-6 (i.e. undergraduate modules for Parts 1-3) and 50% in the case of Level 7 modules offered as part of an Integrated Masters or taught postgraduate degree programme;
• where the piece of work is awarded a mark below the threshold pass mark prior to any penalty being imposed, and is submitted up to three working days after the original deadline (or any formally agreed extension to the deadline), no penalty shall be imposed;
• where the piece of work is submitted more than three working days after the original deadline (or any formally agreed extension to the deadline): a mark of zero will be recorded.

Assessments marked Pass/Fail

• where the piece of work is submitted within three working days of the deadline (or any formally agreed extension of the deadline): no penalty will be applied;
• where the piece of work is submitted more than three working days after the original deadline (or any formally agreed extension of the deadline): a grade of Fail will be awarded.

The University policy statement on penalties for late submission can be found at: /cqsd/-/media/project/functions/cqsd/documents/qap/penaltiesforlatesubmission.pdf

You are strongly advised to ensure that coursework is submitted by the relevant deadline. You should note that it is advisable to submit work in an unfinished state rather than to fail to submit any work.

Formative assessment

Formative assessment is any task or activity which creates feedback (or feedforward) for you about your learning, but which does not contribute towards your overall module mark.

Formative Blackboard tests that assess understanding of the online course, lecture material and practical theory will provide students with feedback so that they have an opportunity to reflect on progress and improve.

Students will be given the opportunity to reflect on their practical work and encouraged to seek 1:1 feedback from practical class leaders / demonstrators during laboratory classes to help improve their practical skills. There will also be opportunities for students to get feedback on scientific writing and referencing from peers / tutors prior to submission of the essay assignment. 

Reassessment

Additional costs