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The University of Southampton
Biological Sciences

Dr Franklin Nobrega BSc, MSc, PhD

Lecturer in Microbiology, Principal Investigator Microbiology

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Dr Franklin Nobrega is a Lecturer in Microbiology within the School of Biological Sciences at the University of Southampton. His research focuses on the arms-race between bacteria and their viruses, the bacteriophages, from a biological, ecological, and therapeutic perspective. He seeks to understand the impact of bacteriophages in shaping natural microbial communities, particularly their role in the evolution of defence and anti-defence mechanisms, and their capacity to modulate bacterial metabolism, especially in biofilm and gut communities. He also works to develop innovative phage therapy approaches to fight antibiotic-resistant bacterial infections.

Career history

2020-Present: Lecturer. University of Southampton, UK
2019-2020: Scientific advisor. SNIPRBiome, Denmark.
2019-2020: Scientific advisor. BGI Group, China.
2017-2020: Postdoctoral fellow. Delft University of Technology, Netherlands.
2016-2017: Postdoctoral fellow. Wageningen University, Netherlands.

Fellowship awards

2020-2021: AHSCC-19Engage. University of Southampton, University Hospital Southampton NHS Foundation Trust, UK.
2019-2020: ZonMw Diabetes Fonds. Delft University of Technology, Netherlands.
2017-2020: Netherlands Organisation for Scientific Research Veni NOW-ALW grant. Delft University of Technology, Netherlands.

Academic qualifications

2013-2017: PhD Microbiology. Wageningen University, Netherlands.
2008-2009: MSc Biotechnology. Faculty of Science and Technology, Portugal.
2003-2007: BSc Biotechnological Engineering, Lusofona University, Portugal

Research interests

Shaping of microbial communities by bacteria and bacteriophage interactions

Defence and anti-defence systems
My research group is interested in the molecular and structural characterization of bacterial defence systems. Currently we study the DISARM class 1 and the membrane-associated KIWA defence systems. We also study phage anti-defence mechanisms and are currently working on the characterization of the smallest anti-CRISPR protein known to date and of a prophage-encoded Cas protein that interferes with the bacterial CRISPR defence. Additionally, we are searching for anti-KIWA phage proteins.

Defence and anti-defence systems in natural environments
We investigate the role of defence and anti-defence systems in natural environments, such as biofilms and the gut. In particular, we are interested in the following questions: what is the real impact of defence systems in natural environments? Is protection given by defence systems as important in biofilms as in planktonic bacteria? Can we identify defence systems expressed exclusively in a biofilm state? Are there links between biofilm and defence system regulation?

Mobilization of defence systems
Additionally, we study the role of gene transfer agents (GTAs) and outer membrane vesicles in the mobilization of defence systems in planktonic and biofilm bacterial populations.

Modulation of bacterial metabolism by bacteriophages

Mechanisms of metabolic modulation
My research group investigates the mechanisms used by phages to hijack the bacterial metabolism in immediate and delayed forms. Currently we are looking at phage proteins that interfere with specific metabolic pathways, in particular those involved in biofilm formation and dispersal. These proteins find multiple biotechnological and medical applications. 

Phage-mediated changes in bacterial metabolism and human health
Dysbalance of the gut microbiome can lead to important cardio-metabolic disorders. The composition of the gut microbiome is affected by multiple factors, among which phages. Fecal microbiota transplantation (FMT) is an established treatment for Clostridium difficilis infections, and an experimental therapy for other gut diseases like colitis, IBS, and even Parkinson. In collaboration with Dr. Hilde Herrema from Amsterdam Medical Center in the Netherlands, we are investigating the role of phages in FMT success using virome (phage) transplantations.

Bacteriophages in localized gut microbial communities
The gut is not a homogeneous environment, and as such the distribution of bacteria and phages can be variable. My research group is studying phage distribution and residence time in different sections of the gut, their influence on the establishment of localized microbial communities (e.g. microcolonies), and their impact on human health.

PhD supervision

Cristian Aparicio-Maldonado (TU Delft, co-supervision)
Thomas Todeschini (supervision)
Rodrigo Gonzalez Linares (supervision)
Simran Krishnakant Kushwaha (Birla Institute of Technology and Science, co-supervision)

Research group


Affiliate research groups

Institute for Life Sciences (IfLS), Computational and Systems Biology

Research project(s)

Exploration of pan-immunity in prokaryotes

Discover novel ways used by phages to strike back against bacterial defences

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Book Chapter

  • Luzia De Nobrega, F., Lavigne, R., & Brouns, S. JJ. (2017). Revival of phage therapy. In J. van Doorn, C. Biemans, J. Luirink, J. van der Oost, B. Oudega, L. Robertson, H. Smit, & P. Willemsen (Eds.), Mighty Microbes - The amazing worlds of microorganisms Stichting Microcanon.



Dr Franklin Nobrega
School of Biological Sciences
Faculty of Environmental and Life Sciences
Life Sciences Building 85
University of Southampton
Highfield Campus
SO17 1BJ

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