Centre for Phage Research
What are bacteriophages?
The word “bacteriophage” is derived from “bacteria” and the Greek word “phagein,” which means “to devour/eat.” Bacteriophages, often simply referred to as phages, are viruses that specifically infect and replicate within bacteria. Unlike other viruses that might target animals, plants, or fungi, bacteriophages have evolved to prey on bacterial cells.
In recent years, bacteriophages have gathered interest for their potential therapeutic applications, especially as antibiotic resistance becomes a growing global concern. Phage therapy, which involves using phages to combat bacterial infections, offers a promising alternative or supplement to traditional antibiotics.
Our mission
The Leicester Centre for Phage Research aims to tackle current and future global challenges with a focus on medicine, infectious diseases, biotechnology, agriculture, food sustainability and climate change. We use multidisciplinary research to isolate, characterise, understand and deliver phages, phage-based technologies and therapeutics. We are working actively with regulators, policymakers and other stakeholders to establish frameworks and pathways to ultimately enable the public to access phage products.
What we do
Bacteriophage isolation
We have experience of isolating bacteriophages against a range of different bacteria. This includes but is not limited too anaerobes (Clostridium difficile, Lactococcus spp), cyanobacteria, Vibrio spp, Escherichia coli, Salmonella spp, Klebsiella spp and Pseudomonas spp.
Bacteriophage cocktail development
We are experienced in developing and optimizing phage cocktails. This includes phage cocktails that have been successfully used in agricultural applications and more recently the development of phage cocktails to target urinary tract infections in humans.
Bacteriophage characterisation
We are experienced in a range of methods for characterization of bacteriophages. This includes imaging (TEM, Atomic force microscopy), standard one-step growth experiments via both culture- and molecular-based approaches, host-infection ranges analyses and stability assays.
Bacteriophage genomics
We have experience of sequencing and analysis of bacteriophages genomes that have been sequenced by a range of sequencing technologies including Illumina, PacBio and Nanopore.
Viromics
We are experienced in the isolation of both viral (phage) DNA and RNA for metagenomic analysis. This includes viromes from diverse sources including mammalian faeces (human, mouse, cow), human airways, soil, animal slurries and a variety of water-based samples. With analysis of viromes from both long read (PromethION, minION, PacBio) and short read sequencing (Illumina).
Modelling of phage-bacteria interactions
We use mathematical modelling to explore how bacterial populations are controlled by phages in complex spatial-temporal environments, focusing on the tropical environmental pathogenic bacteria, Burkholderia pseudomallei and their phages. Among other things, our models can explain and predict seasonal bacterial blooms, spatial distribution of bacteria in the soil environment and effects of climate change on the bacterial distribution in the environment.
Bacteriophage engineering and mutagenesis
We use both random mutagenesis and homologous recombination approaches to understand the function of phage genes. This is both the to develop "better" phages for therapeutic use and understand the basic function of phage genes. To date this work has focused on coliphages and cyanophages.
Microbiome of the human airways
We use observation (metagenomic and 16S sequencing), in vitro (Winogradsky microcosms), and in silico (ecology and population dynamics) approaches to characterise the respiratory microbiome and understand its role in chronic lung diseases (CLDs) like asthma and COPD. Our aim is to build a framework for microbiome-based management of CLDs using phage technologies and inform current phage therapy protocols.
Our computational resources
Millardlab
Monthly, interactive updates of genomes.
Inphared database
Cite: Cook R, Brown N, Redgwell T, Rihtman B, Barnes M, Clokie M, Stekel DJ, Hobman J, Jones MA, Millard A. INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes. Phage (New Rochelle). 2021 Dec 1;2(4):214-223. doi: 10.1089/phage.2021.0007. Epub 2021 Dec 16. PMID: 36159887; PMCID: PMC9041510.
PhageCompass
Various software we have developed with our partners Thomas Sicheritz-Pontén and Bent Petersen.
PhageLeads
Check phage if they are lytic/temperate and contain virulence or antibiotic resistance genes.
Cite: Yukgehnaish K, Rajandas H, Parimannan S, Manickam R, Marimuthu K, Petersen B, Clokie MRJ, Millard A, Sicheritz-Pontén T. PhageLeads: Rapid Assessment of Phage Therapeutic Suitability Using an Ensemble Machine Learning Approach. Viruses. 2022 Feb 8;14(2):342. doi: 10.3390/v14020342. PMID: 35215934; PMCID: PMC8879740.
PhageClouds
Compare phage genomes against large set of other phage genomes.
Cite: Rangel-Pineros G, Millard A, Michniewski S, Scanlan D, Sirén K, Reyes A, Petersen B, Clokie MRJ, Sicheritz-Pontén T. From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs. Phage (New Rochelle). 2021 Dec 1;2(4):194-203. doi: 10.1089/phage.2021.0008. Epub 2021 Dec 16. PMID: 36147515; PMCID: PMC9041511.
PhageBoost
Predict prophages in bacteria via machine learning.
Cite: Sirén K, Millard A, Petersen B, Gilbert MTP, Clokie MRJ, Sicheritz-Pontén T. Rapid discovery of novel prophages using biological feature engineering and machine learning. NAR Genom Bioinform. 2021 Jan 6;3(1):lqaa109. doi: 10.1093/nargab/lqaa109. PMID: 33575651; PMCID: PMC7787355.
PhageCSR
Phage classification system.
Cite: Clokie MRJ, Blasdel BG, Demars BOL, Sicheritz-Pontén T. Rethinking Phage Ecology by Rooting it Within an Established Plant Framework. Phage (New Rochelle). 2020 Sep 1;1(3):121-136. doi: 10.1089/phage.2020.0015. Epub 2020 Sep 16. PMID: 36147824; PMCID: PMC9041459.
TaxmyPhage
Script to assign taxonomy to a bacteriophage at the genus and species level.
Opportunities to join the centre
We welcome folks to train, study, work, or collaborate with us. If you are interested, please contact us at centreforphageresearch@leicester.ac.uk.
PhD fellowships are available every year through the MiBTP, BRC, and AIM doctoral training centres after a selection process.
Students interested in self-funded PhD projects should contact the principal investigator that they want to collaborate with to discuss/develop their projects.