Microbes and the Environment

University of Galway

Course Description

  • Course Name

    Microbes and the Environment

  • Host University

    University of Galway

  • Location

    Galway, Ireland

  • Area of Study


  • Language Level

    Taught In English

  • Prerequisites

    Admission to this course is subject to the agreement of the Head of the Discipline offering the course and will depend on the applicant's academic background in the relevant subject area.

  • Course Level Recommendations


    ISA offers course level recommendations in an effort to facilitate the determination of course levels by credential evaluators.We advice each institution to have their own credentials evaluator make the final decision regrading course levels.

    Hours & Credits

  • ECTS Credits

  • Recommended U.S. Semester Credits
  • Recommended U.S. Quarter Units
  • Overview



    Lecture 1: Microbial Classification Systems
    Importance of microbial classification systems. Domains of life: Bacteria, Archaea and Eukarya. Hierarchial organisation. Phenotypic Classification: Traditional and standard methods for classification and identification of microbes based on appearance, behaviour and cellular composition.

    Lecture 2 & 3: Genotypic and Phylogenetic Classification
    Newer approaches to classification and identification of microbes based on genetic characteristics. Understanding and establishing evolutionary relationships between microbes. Small SubUnit RNA as target molecule for phylogenetics and for identification.

    Lecture 4-7: Microbial Taxonomy and Nomenclature.
    The previous lecture series (Dr. Boyd) has given you an insight into how microorganisms are classified into their various groupings using classical and molecular techniques. Conventionally, bacteria are grouped (systematics) using criteria contained in Bergey?s Manual of Systematic Bacteriology. These tomes (consisting of five volumes) provide the professional microbiologist with the foundations/details of microbial taxonomy. They are far too complex and are perceived as stoical when used as a teaching tool. This series of lectures is designed to give you an insight into the vast diversity of bacteria that are contained in this unique ecosystem called earth. The approach we are going to take is quiet different. Whilst recognisance will be paid to the taxonomic principles contained within Bergey?s manual, we will investigate the characteristics of bacteria under the following headings: (1) Bacteria with industrial applications, (2) Bacteria that are relevant from an environmental perspective, (3) Medically important bacteria and, (4) the Cyanobacteria. The lecture series will mainly be based on chapter twelve of Brock and details will be provided throughout the course of the lecture series on how possible questions should be attempted in the summer examination.


    Lectures 8 to 14 - Animal Viruses
    The composition, morphology and classification of animal viruses. The life cycle of typical animal viruses. Viral disease of Man and animals (including influenza, measles, chickenpox, smallpox, German measles, hepatitis, herpes, rabies, myxomatosis, etc.). Chronic viral infections. "Slow" viruses and prions. Viruses and cancer.


    Lectures 15 and 16:
    The microbial planet. Ecosystems and habitats. What roles do microbes play in the environment? Introduction to microbial ecology.

    Lecture 17:
    Biogeochemistry and biogeochemical cycles ? how do they drive the biosphere? The role of microorganisms in primary production and decomposition.

    Lectures 18 & 19 - Biogeochemical cycling of Carbon, Nitrogen & Phosphorus (1).
    The biological Carbon cycle in terrestrial and aquatic ecosystems. The impact of humans on the carbon cycle ? global warming.

    Lectures 20 & 21 - Biogeochemical cycling of Carbon, Nitrogen & Phosphorus (2).
    LECTURER: Dr. Vincent O?Flaherty
    LECTURE DATE: February 27th & 28th
    The biological nitrogen and phosphorus cycles. Primary microorganisms involved. Environmental consequences of these cycles.

    Lectures 22 & 23 - Waste and wastewater treatment (1).
    Waste treatment - why? Objectives of waste treatment: 1. To destroy/improve organic compounds in waste materials. 2. To destroy pathogens. 3. Biotransformation to maintain environmental quality.

    Lecture 24 - Waste and wastewater treatment (2).
    LECTURER: Dr. Vincent O?Flaherty
    LECTURE DATE: March 6th
    Aerobic and anaerobic wastewater treatment systems and biology. The role of biofilms in these systems.


    Lecture 25 - 27: ? Pasteur and Koch; the founding fathers of Medical Microbiology.
    A historical overview of the roles played Louis Pasteur and Robert Koch in establishing that microorganisms are responsible for decay and disease. Pasteur?s Swan-neck flask experiments and the debunking of the theory of ?Spontaneous generation?. ?Koch?s postulates? in the context of anthrax and tuberculosis.

    Lecture 28 ? The commensal microflora of man.
    The normal (commensal) flora of humans. Factors affecting the profile of microorganisms found on host surfaces. Examination of the microflora found at different anatomical locations including, skin, upper and lower respiratory tract, eye (conjunctiva), gastrointestinal tract and the urogenital tract. Highlight members of the normal flora that are known pathogens.

    Lecture 29 ? Host defence against invading microorganisms: The immune system.
    The human immune system. Specific and non-specific defence mechanisms against microorganisms. Phagocytosis. Anitibodies and antigens. The structures and roles of the different classes of antibodies. The complement system. Primary versus secondary immune responses.

    Lecture 30 ? Anthrax and Bio-terrorism
    A historical overview of bio-terrorism. Routes of infection by Bacillus anthracis and clinical manifestations of anthrax. Practical implications of using B. anthracis as an agent of biological warfare.

    Lectures 31 ? GI infections: Escherichia coli.
    Commensal versus pathogenic E. coli strains. How E. coli strains are characterised by serotype. Enteropathogenic E. coli (EPEC), Enterotoxigenic E. coli (ETEC) and Enterohemorrhagic E. coli (EHEC). Symptoms and prevention of infection.

    Lectures 32 - Helicobacter pylori and ulcers.
    Recent discovery of the causative agent of stomach ulcers in humans: Helicobacter pylori and Koch?s postulates. Clinical symptoms of infection with H. pylori. Strategies used by H. pylori to survive in the human stomach. Detection and treatment of the disease.

    Lecture 33 ? Summary and exam tips.
    Summary and conclusion of the ?Microbes and disease? lectures. Advice on how to approach the end of year written exam in Microbiology. Course feedback questionnaires.

Course Disclaimer

Courses and course hours of instruction are subject to change.

Credits earned vary according to the policies of the students' home institutions. According to ISA policy and possible visa requirements, students must maintain full-time enrollment status, as determined by their home institutions, for the duration of the program.

ECTS (European Credit Transfer and Accumulation System) credits are converted to semester credits/quarter units differently among U.S. universities. Students should confirm the conversion scale used at their home university when determining credit transfer.

Please reference fall and spring course lists as not all courses are taught during both semesters.

Please note that some courses with locals have recommended prerequisite courses. It is the student's responsibility to consult any recommended prerequisites prior to enrolling in their course.


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