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Advanced Topics in Microbiology 2021 – 2022


Dr. Ursula Bond and Dr. Alastair Fleming

The yeast Saccharomyces cerevisiae has long been used as a model system for the study of eukaryotic cells. Recent developments have seen this model system used as a powerful experimental tool to understand complex biological processes, particularly those associated with human diseases. The first part of this course will explore the experimental approaches used to set up a model biological system. With this background information, you will thenreview some of the seminal papers where studies in yeasts have led to important discoveries into the nature of human diseases such as Huntington’s disease and Parkinson’s disease. In the second part of the course, Dr Fleming will discuss how many of the chromatin processes first identified in yeast also exist in human cells and, when they go wrong, contribute to aging and cancer.

Topics discussed by Dr. Bond in first 5 lectures.

1: Yeast as a Model Organism

2: The Yeast Deletion Library: Looking for Phenotypes

3: Finding Connections and Interactions between genes and their protein products

4: Yeasts as a model for Huntington’s and Parkinson’s Disease

5: From model to discovering drugs for Huntington’s disease

Topics discussed by Dr. Fleming in final 5 lectures.

1: A brief history of chromatin research: from obscurity to the cutting edge

2 & 3 : Early studies in yeast which first demonstrated chromatin regulates transcription

4: Chromatin and aging

5: Chromatin and cancer


Carsten Kröger

To respond to environmental changes, the gene expression programs in bacteria must be tightly controlled. In addition to gene regulation by transcription factors or DNA topology, small, non-coding RNA molecules have been established as a class of regulatory elements in the bacterial cell. Through the course of this class, we will discuss current knowledge such as the identification, mechanism of action and biological functions of selected small RNAs and their RNA-binding proteins  in Gram-negative bacteria. Guided by selected research articles, we will follow the cellular path of a regulatory sRNA from expression to target interaction and subsequent degradation. The course involves presentation of primary literature by students and discussions on experimental design and interpretation.


Kim Roberts

Over the last one hundred years there have been several notable pandemics and outbreaks caused by influenza viruses and more recently coronaviruses. These two virus families are structurally very different and yet their modes of transmission are similar, and both can produce zoonotic viruses that cause pandemics. In this course we will explore and compare:

  • The genomes and replication strategies of coronaviruses and influenza viruses
  • Past and current outbreaks and pandemics
  • Routes of transmission
  • Pathogenesis and virulence factors
  • Vaccination strategies


Marta Martins

The rapid emergence of multidrug resistance in bacteria occurring worldwide is jeopardizing the efficacy of available antibiotics, which for decades have saved millions of lives. In addition, the development of new drugs is still declining with pharmaceutical companies curtailing their anti-infective research programs. Antimicrobial resistance is a “silent pandemic” constituting a neglected global crisis that requires urgent attention and action. Appropriate prescription and optimised use of antimicrobials guide the principles of antimicrobial stewardship activities, together with quality diagnosis and treatment, and reduction and prevention of infections. During the current coronavirus disease 2019 (COVID-19) pandemic there are several threats that can affect antimicrobial stewardship activities and drive antimicrobial resistance. Furthermore, hospital admissions increase the risk of health-care-associated infections and the transmission of multidrug-resistant organisms, which in turn leads to increased antimicrobial use. To tackle these issues, there is the need to re-enforce the discovery of new drugs and/or to repurpose old ones. This course will discuss the lack of new antimicrobial compounds to treat multidrug resistant infections as well as the problematic use of antibiotics during the present COVID-19 pandemic . We will focus on the process of discovery and development of new drugs and the reason why thousands of new molecules never reach the market. We will also discuss the use of potential alternative therapeutics that are focused on shifting the current drug discovery paradigm from “finding new drugs” to “combining existing agents”. Some examples of the approaches to be discussed can include host-directed therapeutics; bacteriophage-based therapies; anti-virulence strategies; development of biofilm inhibitors/disruptors; among others. Using this background information, we will review cutting-edge papers where these approaches are discussed, opening the way to the discovery of new drugs or to the repurpose of old ones. The students will have the opportunity to read and discuss fundamental papers in this area and to critically present their view about antimicrobial resistance as well as potential solutions to tackle this public health issue.


Sinéad Corr

An appreciation of the importance of interactions between the human microbiome and the host organism is currently driving research in biology and biomedicine. Microbiome research has gained momentum in recent years, driven by technological advances and improved cost efficiency for analysis. It is widely accepted that the gut microbiome plays a fundamental role in human health and well-being. The constituents of the microbiome have been shown to interact with one another and with the host immune system in ways that influence the development of disease. Models and methods used to evaluate and study the microbiome are critical to developing an accurate understanding of microbiome composition and dynamics and the impact of these for human health. The knowledge gained will enable development of new strategies which leverage applications of the microbiome for new diagnostic techniques and interventional strategies such as personalized medicine. Importantly, as new tools are developed for probing the microbiome and our knowledge grows, a wealth of new questions will arise. This module will take a student-led approach to discuss technological approaches for investigating host-microbiome interactions, as well as recent advances in our understanding of host immunity and microbial influence and arm the student with a broad understanding of the priorities and challenges in microbiome research today. Students will be provided the opportunity to identify and examine cutting-edge research articles, to present the key research findings and critically discuss the implications for the field.


Siobhán O'Brien

Microbes show a remarkable ability to rapidly adapt to harsh and changing environments. Such rapid evolution can have direct consequences for our health and wellbeing. Antimicrobial resistance, vaccine escape and the switch from acute to chronic infection are all driven by the evolution and spread of adapted strains. Our understanding of microbial evolution has been transformed by real-time experimental evolution in the laboratory. This “living fossil record” allows us to examine the drivers of evolutionary change in pathogens, identify novel genomic mutations over evolutionary timescales and quantify the “fitness advantages” conferred by them.

This course will introduce you to the concept of microbial evolution by way of examining and discussing the most recent and cutting-edge literature in the field. You will learn about what drives the rate and likelihood of evolutionary change as well as how we might leverage or “hijack” evolution to minimise the negative effect a pathogen may have on their host. We will take a closer look at one of the longest running evolution experiments in history – twelve flasks of E. coli evolving for over 50,000 bacterial generations by Rich Lenski’s lab at Michigan State University. Expect fitness conflicts, trade-offs, bacterial warfare and invasions.


Michael Beckett

Upon completion of your undergraduate degrees, many of you will enter employment in industry, but what is industry?

Throughout this course we will begin to shed light on the answer to this question. The course will be broadly divided into 2 main parts.

Part 1 will explore the bio-pharmaceutical industry. We will examine the various processes employed by the large multinational corporations with a focus on what your roles may be. We will also explore how microbiology fits into the bio-pharmaceutical industry with a specific focus on topics such as cell culture, microbial cell factories and microbial contamination.

Part 2 will introduce you to the brewing industry. We will follow the industry from grain to glass so you can learn just how complex the process is. We will uncover the intricacies of topics such as brewing biochemistry, yeast management plans and control of microbial contamination within the brewery environment.

Throughout the course you will hear from experts working within industry where they will explain not only their various roles but also the paths they have taken to get there. Upon completion of the course you will have the tools to hit the ground running should you choose this career path.


Maire Ni Leathlobhair

Asexual or clonal reproduction is probably the most widespread and oldest means of cellular propagation. Clonal organisms include not only unicellular organisms such as viruses, bacteria and parasites; they include complex multicellular eukaryotes, indeed animals and even cancers. This course will provide students with a grasp of the evolutionary principles and processes underlying clonal evolution in different organisms and show how considerations of this evolutionary framework can link studies in microbiology, cancer biology, and transmissible disease. Cancers arise via somatic clonal evolution and a large part of this course will explore the dynamics of cancer cell populations during their proliferation, as well as in response to treatment, and instances of how we can use tractable microbial systems to understand these dynamics. We will also consider the consequences of clonality on population and genome structure and the unique features of somatic evolution that challenge the application of insights from studies of clonal evolution in natural populations. Finally, we will look at examples of mammalian cancers that have the innate ability to be communicable and pass horizontally from host to host, behaving more like unicellular pathogens than cancer cells. Throughout the module, we will read and discuss classic papers along with recent and state-of-the-art research on clonal evolution.