Phase variable epigenetic control of strain fitness of starter cultures and probiotics

Lead Research Organisation: University of Leicester
Department Name: Genetics


Preamble: This is an interdisciplinary KTN CASE BBSRC PhD project supervised jointly by two academic supervisors from the Department of Genetics (Marco R Oggioni) and Mathematics (Andrew Morozov) of the University of Leicester UK and by two industrial supervisors at Chr. Hansen A/S in Horsholm Denmark (Ana Rute Neves and Jonas Jacobsen). The student will be based at Leicester, but during the four years the student will be hosted for six months at the Chr. Hansen headquarters and research facility at Horsholm in Denmark.
Background: Phase variable type I restriction modification (R-M) systems have been identified and we have shown that they provide a novel bacterial epigenetic control mechanism that affects both gene expression and important bacterial phenotypes; i.e. in pathogens, these systems were linked to the capacity for generating disease (Manso et al., Nature Communications 2014). The phase variable genetic modules are based on repeated inverted copies of the specificity gene (hsdS) of the R-M system that allows for high frequency recombination conferring the R-M system with multiple different methylation target specificities. These double-hsdS modules are widespread among firmicutes, including bacterial species of industrial relevance for the production of starter cultures or for use as probiotic functional foods. Extensive genomic data is now available, both for bacterial strains already utilised by industry and for strains being screened for their commercial potential. The proposed project will combine the academic partner's expertise gained by studying the phase variable double-hsdS modules in the lactic acid bacterium Streptococcus pneumoniae (Manso et al., Nature Communications 2014) with the vast expertise in bacterial strain phenotyping at Chr. Hansen (Derkx et al., Microb Cell Fact. 2014) and the large number of sequenced genomes available through the industrial partner.
Aims and objectives: The primary aim of the project is to characterise phase variable double-hsdS modules in firmicutes of commercial interest, especially lactobacilli, and to evaluate their impact on strain fitness and metabolic potential. The long term goal of the whole project would be to produce high level scientific data to allow optimisation of quality control and product efficacy of industrially relevant bacteria harbouring these phase variable epigenetic control systems

Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/P504737/1 01/10/2016 30/09/2021
1732410 Studentship BB/P504737/1 01/10/2016 26/07/2021 Joseph David Ralph
Description Phase variable type I restriction modification systems- systems that are capable of switching the methylation patterns (modification) they introduce into DNA- were characterised in both Enterococcus faecalis and the Lactobacillus casei group.

The target site of the phase variable type I restriction systems were identified in Enterococcus faecalis H25 and a strain from the industrial partner. In addition, the transcriptome of variant methylation patterns were also investigated using RNA sequencing.
Exploitation Route The work in Entercoccus faecalis could be used by other researches when selecting genetic tools or in characterisation of virulent populations of Enterococcus faecalis.

The work in the Lactobacillus casei group could be used by the industrial partner as 8 derivatives of their strain were produced in this work.
Sectors Agriculture, Food and Drink,Healthcare

Description FEMS young researcher conference attendance grant
Amount £720 (GBP)
Organisation Federation of European Microbiological Societies (FEMS) 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2017 
End 08/2017
Description High Speed super-resolution confocal laser scanning microscope for sub-diffraction analysis at the multi-user Leicester Advanced Imaging Facility
Amount £283,824 (GBP)
Funding ID BB/S019510/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2019 
End 06/2020
Description Linking bacterial sugar metabolism and cell-to-cell signalling
Amount $399,000 (AUD)
Funding ID DP190102980 
Organisation Australian Research Council 
Sector Public
Country Australia
Start 04/2019 
End 03/2022
Description microbiology society conference attendance grant
Amount £225 (GBP)
Organisation Microbiology Society 
Sector Learned Society
Country United Kingdom
Start 04/2018 
End 04/2018
Title Programs for the genomic analysis of hsdS genes 
Description A set of python scrips for understanding hsdS diversity 
Type Of Technology Software 
Year Produced 2019 
Impact Results are being fed to to two in prep publications 
Description Open day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Demonstrated the research undertaken in a typical microbiology lab and the tools we specifically use in ours. This allowed discussions on the outcomes of undertaking a microbial sciences course
Year(s) Of Engagement Activity 2017,2018