Dr. Andrew Free

Senior Lecturer, Programme Director (M.Sc. Biotechnology)



Senior Lecturer, 2016

Lecturer in Cell and Molecular Biology, 2012

Darwin Trust Research Fellow, 2007-2009

Wellcome Trust Research Career Development Fellow, 2002-2005

Wellcome Trust Advanced Training Fellow, University of Edinburgh, 1998-2001

Wellcome Trust Prize Research Fellow, Trinity College Dublin, Ireland, 1995-1997


B.A. Natural Sciences, University of Cambridge, 1991

Ph.D. Molecular Microbiology, Trinity College Dublin, Ireland, 1995

M.Sc. Environmental Sustainability, University of Edinburgh, 2006

Responsibilities & affiliations

Programme Director, M.Sc. Biotechnology

Research summary

Pure and applied microbial ecology; host-associated and environmental microbiota; anaerobic digestion; anti-microbial resistance; bioremediation

Current research interests

Microorganisms constitute the vast majority of the diversity of life on planet Earth, and perform crucial functions ranging from carbon fixation, biogeochemical cycling and degradation of toxic waste to the maintenance of healthy function in the mammalian gut. We are interested in the basic ecological processes which determine the diversity, functionality and variability in natural microbial communities and in model laboratory systems, and in applying this basic knowledge to improving the performance of microbial devices such as anaerobic digestors [Vicky Hu with the UK Biochar Research Centre (Dr. Ondrej Mašek) and Carbogenics Ltd.] as well as in the mammalian intestine. We study such communities using modern genomic, metataxonomic and metagenomic techniques based on next-generation DNA sequencing, proteomics, fingerprinting techniques and subsequent pure-culture isolation, as well as modelling microbial communities in collaboration with Dr. Rosalind Allen (School of Physics & Astronomy). Being able to engineer microbial communities for improved function will depend on the isolation and characterisation of novel microbial species and the partners they interact with in their natural environments. To this end, we are developing a project to isolate novel methanogenic Archaea with both neutralphilic and acidophilic lifestyles from freshwater sediments (Michael McDonald in collaboration with Dr. James Chong [University of York]). The eventual goal of this work is to enhance the productivity of anaerobic digestor systems using synthetic ecology. Microorganisms are an integral part of the bodies of mammalian hosts, in particular the gastrointestinal tract, where they contribute to metabolic function, immune system development and resistance to pathogens. We have three current projects which investigate these phenomena. Our work on the interaction between the microbiota and nematode parasites in sheep is conducted in conjunction with Dr. Craig Watkins at the Moredun Research Institute, and involves collaboration with veterinary practices, farmers and the James Hutton Institute. We also characterise the microbiota of the unmanaged and well-studied population of Soay sheep on St. Kilda, in collaboration with Prof. Dan Nussey, Dr. Luke McNally and the St. Kilda Soay Sheep Project. Amy Irvine, in collaboration with Dr. Olga Moncayo and NHS Lothian, is investigating the role of the intestinal microbiota in resistance to and recurrence of Clostridium difficile-associated dysbiosis, a major form of hospital-acquired infection. In a new project, Maggie Knight will investigate the microbial ecology of anti-microbial resistance in the natural environment, during wastewater treatment and in human GI tract microbiota.

Past research interests

Previous projects I have been involved in have studied secondary microbial communities in cyanobacterial photobioreactors (with Scottish Bioenergy), the microbial endobionts of planktonic foraminifera (in collaboration with Dr. Clare Bird), and themicrobial ecology of microbial fuel cells. My early work funded by the Wellcome Trust focussed on the role of abundant chromosomal proteins in gene regulation, in particular the H-NS protein of Escherichia coli and the MeCP2 protein in mammalian cells.