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Microbiomes, Microbes and Informatics (MMI)

We are a dynamic group of academics, research fellows and staff, and postgraduate students carrying out research into medical, environmental and industrial microbiology.

We investigate microbiological phenomena ranging from single cell molecular biology, to communities of organisms and their interactions with humans, animals, plants, and the wider environment.

The group has over 25 active research staff and postgraduate students across five research groups led by:

We are highly research-active, generating millions of pounds of research income from research councils, charities, international funders and industry.

These grant awards are consistently translated into high quality research publications (more than 450 publications, 31,000 citations, and a cumulative h index of more than 180) and training for an extensive cohort of staff and students.

We share a cohesive footprint within a £2+ million refurbished area of the School of Biosciences Sir Martin Evans Building on the second floor in the west wing. This comprises large class II certified research laboratories, equipment and tissue culture rooms, a group office area and academic offices.

We welcome approaches by potential fellowship applicants and funded PhD students to host their research and expand our strategic research on microbiomes, microbes and informatics.

Aims

Microbiomes

We investigate a range of microbial systems and explore the interaction of microbes and microbial communities with humans, animals, plants and wider ecosystems.

Microbes

We have specific expertise in a range of bacterial species including Pseudomonas, Burkholderia, Lactobacillus and other probiotic gut species, enteric pathogens (Escherichia coli, Salmonella), and novel un-cultured microbial taxa.

We study microbial communities that interact with humans (the gut, urinary tract and respiratory microbiome), plants (rhizosphere diversity) and multiple natural environments (fresh water and marine sediments), and dissect beneficial interactions that maintain ecosystem health, as well as pathogenic traits that drive infection and disease in a number of settings.

Informatics

We exploit molecular, genomic, post-genomic, bioinformatic and metabolic strategies to explore microbial functions and interactions. Informatic analysis of the large datasets generated by this research is key to driving forward our research.

Our research is organised across five research groups:

Esh Mahenthiralingam group

Cystic Fibrosis Microbiology

We have studied bacterial lung infections in people with cystic fibrosis for three decades, focussing on Pseudomonas and Burkholderia as key pathogens, and more recently broadening this to encompass the wider interactions of the lung infection microbiome. Current research in this area is being led by Dr Rebecca Weiser, Kasia Parfitt and Alice Collins.

Burkholderia genomics, antibiotic discovery, and environmental interactions

Burkholderia are diverse and multi-talented microorganisms and we are investigating their beneficial properties such as the production of novel antibiotics, plant protection and pollutant degradation. Current researchers include Gordon Webster, Alex Mullins, Rachel Rowe, Amal Alswat, Yoana Petrova and Nico Bruyniks.

Industrial and applied microbiology

We have also investigated a number of industrial problems related to microorganisms. A specific focus is the ability of bacteria such as Pseudomonas and Burkholderia to form biofilms, overcome preservative and cause microbial contamination in a range of industrial products. This research is currently led by Edward Cunningham-Oakes.

Julian Marchesi group

This group focuses on the human microbiome and how the microbiota in different niches contribute to host function and initiation of diseases.

The gut microbiome

We have been looking at the role of the gut microbiota, mainly the bacteria, and in particular the metabolites and proteins that they make. This has been looked at in the context of inflammatory bowel disease (IBD) and cancer. Currently Dr Laura Osborne, Triin Õunapuu and Jane Mikhail are looking at IBD and cancer.

The vaginal microbiome

This ecosystem is a much simpler niche, colonised by fewer bacteria, mainly members of the lactobacilli.  We have been looking at their role in pre-term birth and cervical cancer.

Novel models of the gut and liver

We have been exploring the role of oxygen and flow in shaping the response of colonocytes and hepatocytes. Kyle Murphy and Maria Howland are looking at bacteria and metabolites respectively in these new systems.

The skin microbiome

How do the cosmetics that we use interact and affect the growth of the skin microbiota? Hannah Salvage is investigating this interaction with an industrial partner Croda. Duaa Al-Dulaimy is looking at whether lactobacilli can interfere with the pathogenesis of skins pathogens in a wax-moth larvae model.

The oral microbiome

The pathogenesis of yeast and in particular Candida albicans has been shown to be influenced by the bacteria present in the oral cavity. Daniel Morse will be looking at determining how this interaction occurs.

Cedric Berger group

Host pathogen interaction

We are studying the interaction between enteric pathogens - Enteropathogenic Escherichia coli (EPEC), Enterohemorrhagic E. coli (EHEC), Diffusely Adherent E. coli (DAEC), Salmonella enterica and Citrobacter rodentium - and the host cells, focussing on how the pathogens manipulate the host for their own benefit, and in contrast, how the host responds to the infection to circumvent disease.

Rema El-Turke and Jack Alderton are investigating the role of type 3 secretion system effector in the modulation of Rho GTPases. Teresa Paradell is working on the regulation of small RNA during pathogenesis.

Prevention of diarrheal disease

Every year, around 525,000 children will be killed by gut pathogens. Rotavirus and E.  coli bacteria are the two most common etiological agents in low-income countries. However, the most severe illness is associated with bacterial disease caused by EPEC and DAEC. Our aim is to develop vaccines and animal models that are resistant to infection, as strategies to a decrease of the prevalence of diarrheal disease.

Inflammatory bowel disease and cancer

It is suggested that major inflammatory bowel diseases (IBD), Crohn's disease and ulcerative colitis, are linked to the host response to intestinal bacteria, with adherent E. coli the main suspect. Bowel cancer is the fourth most common cancer in the UK and a link between cancer and bacterial infection is emerging, especially with EPEC. Our aim is to understand the molecular mechanisms leading to IBD and cancer after enteric infection.

Andrew Weightman group

Our research examines the genetic adaption of microbes to multiple environmental challenges, including the deep sea and other sediment subsurface microbiology. The group uses a range of molecular and metagenomic techniques to explore microbial diversity in multiple environmental niches. Current research projects include a Knowledge Transfer Partnership with Volac International Ltd. led by Dr Amy Baldwin.

Thomas Connor group

Our research examines microbial pathogen variation to understand evolution and transmission in local and global outbreaks. We have investigated a range of gastrointestinal pathogens (Escherichia coli, Salmonella, Shigella and Clostridium difficile), as well as antimicrobial resistant ESKAPE pathogens.

The group’s research is underpinned by whole genome sequencing and high-powered computing, and we have been working with Public Health Wales to implement genomics pipelines for pathogen identification and surveillance across Wales, and globally in terms of the virus Influenza.

Current members of the research team include Dr Matthew Bull, who helps develop and maintain the bioinformatics systems, and contributes to multiple research projects. Research fellow, Dr. Lu Cheng is exploring scalable Bayesian statistics clustering approaches to examine a number of biological data systems.

Katherine John-Hall is a PhD student comparing antimicrobial susceptibility of pathogens to their encoded antimicrobial resistance gene content, and Aimee Bettridge is a PhD student developing genomic-based diagnostics for cystic fibrosis and other respiratory infections together with Public Health Wales.

Joel Southgate is a PhD student working with Public Health Wales developing bioinformatics pipelines to examine the genomics of the Influenza virus.

We currently have 8 active postdoctoral research projects and 20 postgraduate projects:

Postdoctoral research projects

‘Whole genome bioinformatic analysis capability for animal nutrition’ (Dr Amy Baldwin, Innovate UK KTP sponsored by Volac International Ltd.)

‘Application of scalable Bayesian clustering approaches to examine variation across cellular populations’ (Dr Lu Cheng, Sêr Cymru II - MSCA COFUND fellowship)

‘The functional proteome as a driver and predictor of IBD status: proteases and phosphatases from bacteria drive host health’ (Dr Laura Osborne, Crohn’s & Colitis Foundation Litwin IBD Pioneers Initiative) - Currently on Maternity leave

‘Genomic Analysis of Helicobacter pylori, the upper GI Microbiome and identification of microbes associated with a high intra-tumoural immune response’ (Dr Jane Mikhail, Wellcome Trust ISSF Award)

‘Understanding the contribution of the oral bacterial microbiome toward Candida albicans virulence and associated mechanisms of action’ (Dr Daniel Morse, Wellcome Trust ISSF Award)

‘Harnessing chemical genomics to discover new antibiotics’ (Dr Gordon Webster, Wellcome Trust ISSF Award)

‘Pseudomonas aeruginosa transposon mutant screen – isolating mutants with growth defects in relation to preservative exposure for metabolic screening’ (Dr Gordon Webster, Unilever)

‘Translating novel sampling and molecular-microbiota research diagnostics into clinical practice for cystic fibrosis lung infection’ (Dr Beky Weiser, Wellcome Trust ISSF Award)

PhD projects

‘Probiotic Interaction with Common Pathogens: Understanding the Impact of Probiotics on Pathogen Function and Metabolism within the Host’ (Duaa Al-Dulaimy, Iraqi Ministry of Higher Education and Scientific Research (MOHESR))

‘The biotechnological potential of natural populations of Burkholderia bacteria for antibiotic production’ (Amal Alswat, Taif University and Royal Embassy of Saudi Arabia)

‘Application of genomics to provide culture-free pathogen diagnostics for Cystic Fibrosis and Chronic Obstructive Pulmonary Disease’ (Aimee Bettridge, KESS2 PhD Studentship)

‘Development of PCR and genomic diagnostics for the identification of industrial contaminants’ (Edward Cunningham-Oakes, BBSRC SWBio Industrial CASE DTP PhD Studentship sponsored by Unilever)

‘Modelling the gut barrier in vitro using techniques to improve physiological relevance and translatability’ (Maria Howland, BBSRC SWBio DTP PhD Studentship)

‘Retrospective genomic analysis of pathogenic bacteria to inform public health interventions in Wales’ (Katherine John-Hall, Public Health Wales PhD Studentship)

‘Mapping the Preterm Gut Microbiome to Preterm Neonatal Outcomes’ (Emma Mitchell, RCUK PhD Studentship)

‘Understanding the plant-protective abilities of Burkholderia ambifaria’ (Alex Mullins, BBSRC SWBio DTP PhD Studentship)

‘Assessing the role of dynamic flow in cell culture and response to probiotics’ (Kyle Murphy, KESS2 DTP PhD studentship sponsored by Cultech Ltd.)

‘Using next generation approaches to define epidemiology and develop therapies for the neglected cystic fibrosis lung pathogen Burkholderia multivorans’(Kasia Parfitt, GW4 BioMed DTP MRC PhD Studentship)

‘Building the molecular tool kits to exploit Burkholderia bacteria as biotechnological agents’ (Yoana Petrova, BBSRC SWBio DTP PhD Studentship)

‘Characterisation of novel antibiotics produced by Burkholderia vietnamiensis’ (Rachel Rowe, Life Sciences Research Network Wales PhD studentship)

‘Exploring the Skin Microbiome's Response to Chemicals used in Skin Products’ (Hannah Salvage, BBSRC CASE PhD Studentship sponsored by Croda Europe Ltd.)

‘Developing bioinformatics and modelling approaches for influenza virus whole genome sequence data, with application to surveillance and forecasting’ (Joel Southgate, BBSRC SWBio DTP PhD Studentship)

‘Regulation of small RNA is critical for bacterial enteric infection’ (Teresa Paradell, PhD studentship)

MRes/MPhil projects

Characterisation of the beneficial interactions of Burkholderia bacteria with plants (Nico Bruyniks)

‘Understanding phenotypic and genetic interactions of pathogens in the cystic fibrosis lung infection microbiome’ (Alice Collins)

‘Isolation of protease producing bacteria to determine their role in inflammatory bowel disease’ (Triin Õunapuu)

‘Manipulation of RhoGTPases by enteric pathogens’ (Rema El-Turke and Jack Alderton)

Academic staff

Professor Eshwar Mahenthiralingam

Professor Eshwar Mahenthiralingam

Co-Director of Research

Email:
mahenthiralingame@cardiff.ac.uk
Telephone:
+44 (0)29 2087 5875
Professor Julian R Marchesi

Professor Julian R Marchesi

Professor of Human Microbiome Research at Cardiff University and Professor of Digestive Health at Imperial College London

Email:
marchesijr@cardiff.ac.uk
Telephone:
+44 (0)29 2087 4188
Professor Andy Weightman

Professor Andy Weightman

Head of Organisms and Environment Division, Professor

Email:
weightman@cardiff.ac.uk
Telephone:
+44 (0)29 2087 5877
Dr Thomas Connor

Dr Thomas Connor

Reader

Email:
connortr@cardiff.ac.uk
Telephone:
+44 (0)29 2087 4147
Dr Cedric Berger

Dr Cedric Berger

Senior Lecturer, Associate Theme Lead for Immunology, Infection and Inflammation

Email:
bergerc3@cardiff.ac.uk
Telephone:
+44 (0)29 2087 4829
Dr Gordon Webster

Dr Gordon Webster

Senior Technician

Email:
websterg@cardiff.ac.uk
Telephone:
+44 (0)29 2087 7011
Dr Jane Mikhail

Dr Jane Mikhail

Honorary Research Associate

Email:
mikhailj@cardiff.ac.uk
Telephone:
+44 (0)29 2087 211
Dr Daniel Morse

Dr Daniel Morse

Research Associate

Email:
morsedj@cardiff.ac.uk
Dr Laura Osborne

Dr Laura Osborne

Research Associate

Email:
osbornel4@cardiff.ac.uk
Telephone:
+44 (0)29 2087 4921
Dr Amy Baldwin

Dr Amy Baldwin

Research and Development Scientist

Email:
baldwinaj@cardiff.ac.uk
Telephone:
+44 (0)29 2087 4648
Dr Lu Cheng

Dr Lu Cheng

COFUND Fellow

Email:
chengl7@cardiff.ac.uk
Telephone:
+44 (0)29 2087 4648

Postgraduate students

Kyle Murphy

Research student

Email:
murphyk5@cardiff.ac.uk
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Hannah Salvage

Research student

Email:
salvagehe@cardiff.ac.uk
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Aimee Bettridge

Research student

Email:
bettridgeas@cardiff.ac.uk
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Joel Southgate

Research student

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Maria Howland

Research student

Email:
howlandm1@cardiff.ac.uk
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Nico Bruyniks

Research student

Email:
bruyniksn@cardiff.ac.uk
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Alex Mullins

Research student

Email:
mullinsa@cardiff.ac.uk
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Kasia Parfitt

Research student

Email:
parfittkm@cardiff.ac.uk
Photo of Rachel Rowe

Rachel Rowe

Research student

Email:
rowera@cardiff.ac.uk
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Yoana Petrova

Research student

Email:
petrovayd@cardiff.ac.uk
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Amal Alswat

Research student

Email:
alswata@cardiff.ac.uk