Microbiome
The microbiome is a term used to describe the community of microorganisms that live on or within a host organism. It is increasingly being recognised as in important contributor to human health and disease.
At the NIBSC, our microbiome section is focused on understanding how current microbiome therapeutics work, how the microbiome can cause disease, and how we can exploit the microbiome to deliver novel therapeutics. We are also leading an extensive standardization program to generate the first World Health Organization reference reagents for the microbiome to try and solve the reproducibility crisis in the microbiome field.
We work closely with the Next Generation Sequencing team at NIBSC to perform high-throughput sequencing experiments and are particularly interested in understanding how microbes interact with one another and the human host. To facilitate this, we have a large anaerobic cultivation facility and are developing several model systems.
Please contact us if you have any questions about our work, would like to collaborate with us, or would like to join one of our large international collaborative studies. If you are a student or postgraduate with your own funding and are interested in undertaking a placement with us, please get in touch, although we cannot guarantee an offer.
Our research
Our research projects are primarily funded by Innovate UK, DHSC, MRC and NIHR. We collaborate with a number of academics, NHS trusts, and industrial partners to deliver state-of-the-art research and reference reagents. All projects listed here are facilitated by productive collaborations across the NIBSC divisions of Analytical and Biological Sciences, Bacteriology, Virology, and Biotherapeutics.
Microbiome standardisation
We are leading one the world’s largest microbiome standardisation programs as part of the World Health Organization Biological Standardisation program to develop the first WHO International Reference Reagents for the microbiome. The microbiome field has no accredited or certified reagents to control for biases in experiments which has led to a reproducibility crisis across the field.
We are developing DNA and Whole-Cell Standards for analysis of the Gut, Oral Cavity, Nasopharynx, Skin, and Vaginal microbiomes. The program will yield 12 reference reagents over the next 24 months (by the end of 2022) which will be available from the NIBSC catalogue.
This work is partly dependent on large international collaborative studies which can require as many as 20 international partners to validate reagents. If you have the capacity to sequence and test our reagents and would like to be part of International Collaborative studies, then we are interested in hearing from you.
Microbiome and chronic gut disease
We have a longstanding collaboration with The University of Warwick and University Hospitals Coventry and Warwickshire researching how the microbiome causes chronic disease in the gut.
Our previous work has identified key microbial imbalances in the gut during Inflammatory Bowel Disease (IBD) and has delineated how location and severity influence microbiome composition during IBD. Currently, we are researching treatments for chronic bowel diseases such as projects investigating how novel probiotics can potentially change the microbiome in patients with Irritable Bowel Syndrome (IBS) and whether Faecal Microbiota Transplantation (FMT) can be used to treat Bile Acid Diarrhoea (formerly termed Bile Acid Malabsorption). These projects focus on the mechanistic role bacteria play in the regulation of host metabolism.
Microbiome and cancer
We work with the MRC Centre for Drug Safety Science at The University of Liverpool to determine whether changes in the microbiome are responsible for adverse reaction events observed during immune checkpoint inhibitor (CPI) therapy for cancer. The microbiome is known to have an immune-regulatory role, and patients are often on therapies before CPI which can disrupt the resident microbiota. Work here could give insights into how to improve CPI efficacy and how to prevent adverse reaction events to CPI.
We also have an interest in colorectal cancer and have recently embarked on a project with UHCW and Warwick University to develop biomarkers for colorectal cancer based on changes in the microbiome. These biomarkers could either be the bacteria themselves or measured as volatile organic compounds which changes in the microbiome can be responsible for.
Microbiome and antimicrobial resistance
Antimicrobial resistance (AMR) is one of the biggest challenges facing us in the 21st century. Reducing our dependency on antibiotics is critical to preserving them. FMT is a therapy which has shown remarkable efficacy at treating antimicrobial-resistant C. difficile infections. Despite this, no known mode of action for FMT is known. We are collaborating with the Microbiome Treatment Centre at The University of Birmingham to try and better understand this biological medicine and develop markers for its efficacy.
Additionally, we are researching whether FMT can be used to eliminate carriage of multidrug-resistant organisms. We are working with King’s College London and Guy’s and St Thomas’ NHS Trust as part of the FERARO clinical trial looking at the feasibility of giving capsulized FMT to help eradicate AMR. Together we will be performing exploratory research to understand how FMT impacts AMR load in the gut using the standardized metagenomic pipelines developed at NIBSC.
We also conduct research into the environmental dimension of AMR. The One Health approach to studying AMR is now recognized as the only way to prevent the widespread dissemination of AMR genes throughout our communities. We are collaborating on a large project led by The University of Warwick, University of Exeter, and UK Centre for Ecology and Hydrology investigating AMR in the UK waterways and the risk this could pose to human health.
Microbiome and vaccination
The microbiome has a well-characterised role in influencing the human immune response. Routine vaccination will usually have a variation in responses across the human population. We work on a project with the Live viral vaccines group at NIBSC to better characterise the role of the microbiome in shaping the response to vaccination against Rotavirus in infants.
We are also involved in a range of other projects such as investigating how the microbiome can influence the response to Factor VIII used for the treatment of haemophilia A and developing rapid sterility tests to assure the quality of short-life medicines. Please contact us to find out more.