Research

Dr Christopher Quince

Lecturer in Biological Systems Modelling

Metagenomics coupled to next generation sequencing has transformed our understanding of the microbial world. It has allowed us to directly determine community structure and function in situ from the DNA of the organisms present. This is revolutionising microbial ecology. My research consists of the development of improved statistical and bioinformatics tools for interpreting this sequence data.

These tools exploit advanced methods from machine learning and Bayesian statistics. I work on both 16S rRNA gene amplicon data, having developed the AmpliconNoise algorithm for error removal from 454 pyrosequenced amplicons http://code.google.com/p/ampliconnoise/ and shotgun metagenomics for example the CONCOCT algorithm for automated genome extraction from shotgun metagenome reads https://github.com/BinPro/CONCOCT. In addition, I also develop Bayesian statistical models for interpreting microbial community structure addressing questions such as are enterotypes real features of the human gut microbiome and are microbial communities neutrally assembled? In collaboration with numerous groups around the world I apply these methods to both environmental and host-associated microbial communities.

For instance, with Dr Konstantinos Gerasimidis (University of Glasgow) and Prof Nick Loman (University of Birmingham) I have resolved the changes in gut microbiota composition of children with Crohn's disease during treatment with exclusive enteral nutrition. This could potentially lead to improved therapeutic strategies.

With Dr Gavin Collins (University of Galway) I study the structure of anaerobic digestion reactor communities. More efficient AD digesters will provide more effective biogas production from wastewater, reducing pollution and providing a renewable energy resource. I am currently employed as an MRC Principal Research Fellow as part of the Cloud Computing for Microbial Bioinformatics (CLIMB) consortium.

Natasha Turner

PhD Student

I completed my undergraduate degree in microbiology from the University of Glasgow in 2017 and I am currently a PhD student at the University of Glasgow working with Professor Roe and Dr Gerasimidis. I am studying the role of D-amino acids in bacterial pathogenesis and will be looking at the dietary consequences these amino acids play on the microbiome.

Hannah Baer

PhD Student

Originally from Hamburg (Germany) I moved to Scotland to start an Undergraduate degree in Biochemistry at the University of Dundee. This BSc sparked my interest in Immunology, so I proceeded to do a MSc in Immunology and Inflammatory Disease with the University of Glasgow. After finishing my master’s course, I decided to stay at the University of Glasgow and joined the Milling Group for a PhD to investigate different disease mechanisms in Inflammatory Bowel Disease.

Rebecca Totterdell

PhD Student

I completed my undergraduate degree in Physiology at the university of Aberdeen in 2017, where I became interested in the role of nutrition in the prevention of chronic disease. Following this, I came to the University of Glasgow to study a postgraduate degree in MSc Human Nutrition, specialising in Public Health Nutrition. I decided to focus my career in developing interventions and using research to influence policy makers to improve health at population level. In 2018, I started my PhD with Dr Konstantinos Gerasimidis, Dr George Raptis and Dr Evi Germeni. The project involves developing a protocol for Scottish schools to help staff safely manage pupils with severe allergies. The comprehensive protocol will cover prevention, recognition and treatment of emergencies.

Rodanthi Papadopoulou

Research Assistant

I have a BSc in Nutrition from Leeds Metropolitan University and a BSc (Hons) in Dietetics from the University of Hertfordshire. In addition to that I obtained my MSc in Human Nutrition with a specialization in Clinical Nutrition from the University of Glasgow. I work as a research assisstant in the department of Human Nutrition at the University of Glasgow. My role is such that I work on numerous projects in areas interested in the role of the gastrointestinal micro- and myco-biome in various chronic diseases including Crohn's disease, ulcerative colitis and alopecia.

Dr Michael Logan

Research Assistant

I completed my undergraduate degree from the University of Glasgow in immunology in 2014, followed by an MRes in biomedical sciences the following year. I was then fortunate to begin my PhD in Dr Gerasimidis group. My PhD project, titled the BIG (bacteria, inflammation, and gastroenterology) study focuses on the microbiome of children newly diagnosed with inflammatory bowel disease (IBD). Crohn’s disease is the leading form of IBD in children, the first line treatment of which is a dietary therapy called exclusive enteral nutrition (EEN). I study microbiome changes throughout this therapy, as well as having a specific interest in the post EEN diet in these children.