David Clarke APEX

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David Clarke

David Clarke graduated with a BSc in Biotechnology from Dublin City University in 1989 and he was awarded his PhD in Microbiology from the National University of Ireland in Maynooth in 1993. He then travelled to France where he was awarded an International Traveling Prize Fellowship by the Wellcome Trust to undertake post-doctoral research in the laboratory of Professor Barry Holland who was based at the Institut de Génétique et Microbiologie in Université Paris-Sud. In September 1998 David briefly returned to the Department of Biology at NUI Maynooth as a Lecturer before joining the faculty of the Department of Biology and Biochemistry at the University of Bath, UK in January 2000. He was promoted to Senior Lecturer in September 2004 before returning to Ireland in February 2007 as a College Lecturer in the School of Microbiology at UCC. Dr Clarke is currently Director of the BSc Biotechnology programme at UCC and he is also a Funded Investigator in the APC Microbiome Institute. Click here to see Dr Clarke’s full CV, including publications, on ORCID.


Research Projects in the group

  1. Molecular analysis of beneficial bacteria-host interactions

The major research theme of the Clarke group is the identification and characterization of molecular mechanisms that underpin bacteria-host interactions. We are particularly interested in non-pathogenic interactions as it is likely that most of the interactions between multicellular hosts and their microbial partners are mutually beneficial. To facilitate this work, we use model systems and we focus on the interaction between mammals and commensal Escherichia coli and Bacteroides spp. And the interaction between Photorhabdus luminescens and its invertebrate nematode host. All of our work is based around the application of cutting-edge technologies such as gene knock-out technologies, TraDIS libraries with NGS sequencing and RNAseq, to address key questions in each of these model bacteria-host systems:


  1. Escherichia coli: coli is a facultative bacterium found in the gut of mammals, including humans. Amongst other functions, E. coli plays an important role in protecting the gut from infection by pathogenic bacteria. We are interested in identifying factors in E. coli that are important for colonization of, and growth within, the mammalian gut.
  2. Bacteroides spp.: Approximately 50% of the human gut microbiome is composed of Bacteroides suggesting an important role for this bacterial genus within this ecosystem. Human babies are born sterile and they obtain their microbiome from their environment in a process called transmission. We are interested in identifying the molecular mechanisms that facilitate the transmission of Bacteroides between hosts, particularly from mother to child.
  3. Photorhabdus luminescens: Photorhabdus is a highly virulent pathogen of insects that also has a mutualistic (symbiotic) association with nematodes from the family Heterorhabditis. Together the bacteria and nematode parasitize a wide range of soil-dwelling insect larvae and the bacteria-nematode complex is commercially exploited as a biocontrol agent. Photorhabdus are absolutely required for normal nematode growth and development whereby the bacteria provide essential nutrients and signals to the nematode. We are interested in identifying the genes in Photorhabdus that are required for the mutually beneficial bacteria-nematode association.


  1. Bioprospecting the human gut microbiome.

The human gut contains 1013-1015 bacteria (i.e. the microbiome) that contribute a significant metabolic function to their host. The metabolic potential of the microbiome is under-exploited and, therefore, using an approach based on functional metagenomic screens, we are undertaking targeted bioprospecting and biomining in the human gut microbiome for the discovery of novel metabolic functions and bioactive molecules. To do this we are exploiting existing metagenomic libraries of the human gut microbiome and a high-throughput robotics platform available within the APC Microbiome Institute.


Contact details: E-mail: david.clarke@ucc.ie; Tel: +353 21 4903624