The Microbiome

Gastrointestinal illness continues to be a considerable cause of morbidity in the UK and recent estimates are of up to 17 million sporadic, community cases of IID and 1 million GP consultations annually. Current diagnostic strategies do not detect an aetiological agent in the majority of cases and even when advanced PCR based procedures are used, a pathogen is detected in only 40% of faecal specimens submitted from patients with diarrhoea in the community. Metagenomics allows the production of genomic sequence information from populations of micro-organisms, as well genomic information on the host. This approach has become available with the advent of next generation sequencing. Metabolomics using high throughput nuclear magnetic resonance (NMR) and mass spectrometry (MS) technologies can provide detailed information on the function of the microbiome in diseased state. However, potential public health benefits from these strategies have not yet been realized and require further investigation

Overall objectives of the theme:

  1. To generate an archive of faecal specimens from patients with gastrointestinal disease together with associated epidemiological information and state of the art microbiological diagnostics.
  2. Evaluate metagenomic and metabolomic profiles of patients and pathogens for diagnosis, and identification of biomarkers, of disease.
  3. Establish the usefulness of metagenomics and metabolomics to provide additional and novel information to inform public health interventions.
  4. Generation of –‘omics’ derived biomarkers of infection, vulnerability or risk of relapse.

Theme Leaders:

Professor Arjan Narbad

Research Group Leader for
Quadram Institute

Professor James McLauchlin

Lead Public Health Microbiologist (Director) Food Water and Environmental Microbiology Laboratory Services, Public Health England


Dr Lee Kellingray

Researcher for Quadram Institute

Henry Whiley

Microbiology Research Technician for Quadram Institute

PhD student:

Saskia Neuert