Award details

Microbial pathogens: from Ecology to Synthetic Biology

Reference	BBS/E/F/00044414
Principal Investigator / Supervisor	Professor Mark Pallen
Co-Investigators / Co-Supervisors
Institution	Quadram Institute Bioscience
Department	Quadram Institute Bioscience Department
Funding type	Research
Value (£)	472,803
Status	Completed
Type	Institute Project
Start date	01/04/2017
End date	31/03/2022
Duration	59 months

Abstract

Objectives: to understand microbial communities and to exploit synthetic biology to turn E. coli into a smart probiotic capable of improving such communities. We have investigated the ecology of complex microbial communities using high-throughput sequencing on the Illumina platform in two settings: the gut microbiome in critically ill patients from the UK (focusing on drug-resistant pathogens) and the gut microbiome in ticks (focusing on potential vertebrate pathogens and tick endosymbionts). The establishment of laboratory and bioinformatics workflows have allowed us to document the changes in the microbial ecology of adult critically ill trauma patients during their stay in the Intensive Care Unit at the Queen Elizabeth Hospital in Birmingham, performing shotgun metagenomic sequencing of serial faecal samples. We have also cultured E. coli isolates from these samples and genome-sequenced multiple colony-picks to investigate within-host diversity and ecology and evolution for this important organism. On ticks from Palestine, we have employed a two-stage surveillance protocol, initially screening pools of ticks using 16S rRNA sequencing, followed by shotgun metagenomics to investigate genomic diversity and population structure of microbes from the tick gut. We have detected and characterised a range potential pathogens or endosymbionts in ticks, including representatives of the genera Rickettsia, Anaplasma, Francisella and Coxiella. In pursuit of our goal of re-engineering E. coli, we have focused on the bacterial flagellum as a tool for surface display of enzymes and other globular proteins. To determine the constraints to the size of flagellin, we have carried out and published a survey of natural diversity in the size of flagellins and flagellar filaments. We have also created constructs needed for expression of flagellins incorporating enzymatic domains in E. coli and shown that hybrid flagellins can be used to express enzymatic activity.

Summary

unavailable

Committee	Not funded via Committee
Research Topics	Microbiology, Synthetic Biology
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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