Colonisation Resistance

One of the fundamental roles the microbiota plays is resisting infection by invading pathogens. However, it is currently unclear how different members of the early life microbiota mediate these beneficial effects, or how pathogens overcome these responses to cause disease.

Cho Zin is focusing on understanding iron sequestering systems within Bifidobacterium, which we expect to be intrinsically linked to colonisation ability and subsequent inhibition of enteric pathogens. Using global transcriptomic approaches coupled with in vitro assays, we are identifying iron-responsive genes and iron (including lactoferrin) uptake pathways in Bifidobacterium, and employing competition assays (in vitro and in vivo) to determine how this impacts critical colonisation resistance against pathogens including E. coli and Salmonella.

Raymond is interested in Clostridium perfringens, an enteric pathogen in both animals and human known to secrete >20 toxins. Clinically it is associated with intestinal diseases including food poisoning diarrhoea, enteritis necroticans and preterm necrotising enterocolitis (NEC). Using WGS and phenotypic in vitro and in vivo models, we are seeking to understand the underlying mechanisms of Clostridium perfringens-associated gut pathogenesis, with the aim of using these data to design microbiota therapies against this pathogen.

Shab is a bioinformatician who is working on a number of projects from a bacterial and host perspective using his extensive experience of next generation sequencing (NGS) data handling and visualization. In the context of colonization resistance, Shab is leading on development of new pipelines to probe RNASeq data to understand the genetic mechanisms behind protective anti-infection responses.

Cristina is concentrating on understanding the effect that antibiotics have on the gut microbiota of extremely low birth weight (ELBW) preterm infants, which may be linked with increased susceptibly to life threatening diseases such as NEC. Using a variety of NGS approaches (including 16S rRNA and shotgun metagenomics sequencing) and molecular microbiology, we are identifying how specific antibiotic regimens impact the bacterial populations present in the preterm gut, and how antibiotic usage may contribute to the ‘resistome’ i.e. carriage of antimicrobial resistance and virulence genes in the early life microbiota.