The ecology and evolution of microbial immune systems

Facing the therapeutic impasse of antibiotics, farming systems, including aquaculture, should consider the extraordinary resource of phages, natural bacterial predators, for environmentally friendly practices. Sustainable and safe use of phages requires an understanding of their specificity and evolution. However, our knowledge of phage infection mechanisms is mainly based on model systems in laboratory conditions, which do not reflect the enormous diversity that exists in nature.

Using natural populations of marine bacteria (vibrios) infecting oysters, we have shown that most phages have a narrow host range. Their specificity depends first on their ability to bind to the host surface and second on their capacity to resist intracellular defence mechanisms. In the case of the oyster pathogen Vibrio crassostreae, we can track coevolutionary lineages in the marine environment. These are phage species capable of adsorbing specifically to clades nested within V crassostreae. I will present preliminary results from a follow-up of these lineages in a new time-series sampling and genomic analyses that allow us to propose evolutionary scenarios.

Emerging resistance to phages in nature primarily results from horizontal gene transfer. We have discovered a family of phage satellites, named Phage-Inducible Chromosomal Minimalist Islands (PICMIs), which are widely distributed in the Vibrionaceae family. PICMIs are characterized by their reduced gene content, lack of genes for capsid remodelling, and the packaging of their DNA as a concatemer. These islands integrate into the bacterial host genome adjacent to the fis regulator and encode three core proteins essential for excision and replication. PICMIs rely on virulent phage particles to spread to other bacteria and protect their hosts from competitive phages without interfering with their helper phage. The discovery of PICMIs highlights the necessity of fully characterizing virulent phages and their host producers to prevent the spread of satellite-mediated resistance in phage therapy.

In conclusion, exploring natural populations of phages and bacteria is essential for developing fundamental knowledge, providing a solid basis for informed consideration of new therapeutic avenues in the fight against pathogens, while preserving the delicate balance of the microbial ecosystem.

Professor Frederique Le Roux, University de Montreal, Canada

Professor Frederique Le Roux, University de Montreal, Canada

Dr Le Roux explores the paradoxical sustainability of parasitism through her research on various microbes. She completed her doctoral thesis on the human Epstein-Barr virus at the Ecole Normale Superieure of Lyon and conducted postdoctoral research at the Institut Gustave Roussy. Her subsequent work includes studying protozoan parasites of bivalve molluscs at Ifremer, and Vibrio bacteria pathogenic to oysters and shrimp corals at the Institut Pasteur in Paris, Harvard Medical School in Boston, and the Roscoff Marine Station. More recently, she has focused on vibriophages.

Since September 2023, she has held the Canada Research Chair of Excellence in the Eco-Evo-Patho of Microbes in Nature and serves as a Professor at the University of Montreal. As an IVADO member, she and her team investigate the mechanisms and evolution of interactions between bacteria and their phages in natural populations.

The evolution of all forms of life is a history of the relentless conflict between hosts and parasites. Viral parasites of bacteria, known as phages, are key components of all ecosystems and profoundly influence the biology of their bacterial hosts. Phages select for bacteria that evade phage predation by deploying elaborate and mechanistically diverse defence systems, the full breadth of which is only beginning to be realised. Phages also drive the mobilisation and dissemination of genetic material. Yet, despite the central role of phages in microbial evolution and ecology, molecular insight into the reciprocal dynamics of phage-bacterial adaptations in nature is lacking, particularly in clinical contexts. As a direct consequence, the discovery of phage-encoded defence inhibitors dramatically lags behind the known arsenal of bacterial defences. In partnership with international collaborators, my lab has established a longitudinal collection focused on the diarrheal pathogen, Vibrio cholerae, and the lytic phages that prey on this pathogen as it causes disease in humans. Leveraging genomic and mechanistic approaches, we use this tractable platform to gain an in-depth understanding of how these interacting microbes coevolve within the context of human infection. I will discuss mechanisms of defence in epidemic V cholerae mediated by parasitic mobile genetic elements and how phage-encoded mechanisms countering these elements have driven their diversification in epidemic V cholerae. 

Dr Kim Seed, University of California, USA

Dr Kim Seed, University of California, USA

Dr Kim Seed is an Associate Professor in the Department of Plant and Microbial Biology at the University of California, Berkeley. Professor Seed’s laboratory investigates how phages impact the evolution and selection of epidemic Vibrio cholerae, the causative agent of cholera.

The Phage Anti-Restriction Induced System (PARIS) was first identified within hotspots of anti-phage defence systems carried by satellites of the P4 family. There it acts as an anti-anti-restriction system by blocking the infection of phages carrying anti-restriction proteins such as the T7 Ocr. PARIS is composed of a 53 kDa ABC ATPase (AriA) and a 35 kDa TOPRIM nuclease (AriB) that assemble into a 425 kDa supramolecular immune complex. We use cryo-EM to determine the structure of this complex which explains how six molecules of AriA assemble into a propeller-shaped scaffold that coordinates three subunits of AriB. ATP-dependent detection of foreign proteins triggers the release of AriB, which assembles into a homodimeric nuclease that blocks infection by cleaving the host tRNALys. Phage T5 subverts PARIS immunity through expression of a tRNALys variant that prevent PARIS-mediated cleavage, and thereby restores viral infection. PARIS is one of an emerging set of immune systems that target tRNA to trigger translational arrest. It also belongs to a broader family of systems that employ ABC ATPases to sense viral infections.

Professor David Bikard, Institut Pasteur, France

Professor David Bikard, Institut Pasteur, France

David Bikard is the head of the Synthetic Biology lab at the Institut Pasteur in Paris. He obtained an engineering degree from AgroParisTech and a PhD from Paris Diderot University for his work performed at the Institut Pasteur on the integron bacterial recombination system. He then joined the laboratory of Luciano Marraffini at the Rockefeller University as a postdoctoral fellow where he started to work on CRISPR systems. David is interested in the genetic innovation that occurs as a result of the competition between bacteria and phages and how it can be harnessed for biotechnological applications.

Microbial immune systems play a crucial role in protecting microbes from foreign mobile genetic elements (MGEs) such as bacteriophages, satellites, and plasmids. These defence mechanisms can be readily acquired or lost by bacteria, facilitating their adaptation to various threats. Interestingly, many microbial immune systems are themselves encoded by MGEs, linking their distribution directly to the movement of these MGEs. However, not all immune systems are associated with MGEs; some are integrated into different regions of bacterial chromosomes. This raises intriguing questions about the transfer mechanisms of these chromosomally encoded immune systems between bacterial strains. 

In this talk, we will explore the roles of lateral transduction and lateral cotransduction in the mobility of chromosomal defence islands that harbour multiple immune systems. Lateral transduction, a robust gene transfer process mediated by bacteriophages, enables the transfer of large segments of bacterial DNA from one bacterium to another. Lateral cotransduction, a more recently described mechanism, further expands our understanding of gene mobilisation facilitated by phage-inducible chromosomal islands (PICIs). 

We will examine how these processes contribute to the horizontal gene transfer of immune systems across bacterial populations, and their impact on bacterial adaptation and evolutionary dynamics. Our findings will illuminate the complex interactions between phages and bacteria, revealing how these interactions govern the genetic flow and diversity of immune systems within microbial communities. Understanding these mechanisms is vital for gaining insights into the spread of resistance traits and the ongoing evolutionary arms race between microbes and their viral predators.

Professor José Penades, Imperial College London, UK

Professor José Penades, Imperial College London, UK

Professor Penadés studies the emergence and evolution of clinically significant bacteria. His research team is renowned for their insights into how bacteriophages (viruses that target bacteria) and other mobile genetic elements facilitate bacterial chromosomal gene transfer, driving bacterial evolution. He discovered the most potent mechanism of bacteriophage-mediated gene transfer to date: lateral transduction, which makes bacterial chromosomes more mobile than traditional mobile DNA elements.

Professor Penadés also uncovered and studied the transfer mechanism of a widespread and clinically critical family of genetic elements in various bacterial pathogens: Phage-Inducible Chromosomal Islands (PICIs). His lab found that PICIs use a new, highly adaptable form of gene transfer, distinct from lateral transduction, termed lateral cotransduction. These findings enhance our understanding of genetic mobility and its impact on bacterial adaptation and virulence.

The Latin American cholera epidemic, which originated in Peru in 1991, was driven by the West African South American (WASA) lineage of the 7th pandemic O1 El Tor Vibrio cholerae. This lineage is characterized by two genetic signatures: the WASA-1 prophage and a novel set of genes on the Vibrio seventh pandemic island II (VSP-II). 

Our study reveals that these elements encode diverse anti-phage defence systems. Particularly noteworthy is the WASA-1 prophage, which contains a two-gene system termed WASA OLD-ABC-ATPase REase – WorAB, providing resistance against the major predatory phage of pandemic V. cholerae, phage ICP1. We demonstrate that the WorAB system is activated early during infection and functions through abortive infection by halting translation. Furthermore, we uncover that the WASA-specific genes carried on VSP-II encode two additional defense systems: a modification-dependent restriction system targeting bacteriophages with modified genomes, and a novel variant of the Shedu defense system. 

Our findings shed new light on the evolution of pandemic cholera strains and suggest that anti-phage defence systems may have contributed to the success of this major epidemic lineage, which caused more than 1.2 million disease cases in South America in the 1990s.

Professor Melanie Blokesch, Swiss Federal Institute of Technology Lausanne (EPFL), Switzerland

Professor Melanie Blokesch, Swiss Federal Institute of Technology Lausanne (EPFL), Switzerland

Melanie Blokesch is a Professor at the Swiss Federal Institute of Technology Lausanne (EPFL) in Switzerland. Her research focuses on understanding the complex evolutionary pathways of bacteria in natural environments, particularly their transition into human pathogens. She primarily investigates Vibrio cholerae, the causative agent of cholera, and Acinetobacter baumannii, a nosocomial pathogen. 

Dr Blokesch earned her PhD from Ludwig Maximilian University Munich and conducted postdoctoral research at Stanford University before joining EPFL in 2009 as Head of the Laboratory of Molecular Microbiology. Currently, she serves as Director of the Global Health Institute at EPFL.

Bacterial genomes vary extensively in the defence systems they encode, including CRISPR-Cas systems which are present in only ~50% of Pseudomonas aeruginosa genomes. The selective drivers of this variation are not fully understood. Using a large panel of diverse lytic phages we show that the fitness benefit of CRISPR-Cas adaptive immunity varies according to phage identity and function in predictable ways unlinked to known anti-CRISPR systems. The fitness effect of CRISPR immunity was positively associated with the presence of spacers targeting the phage but was negatively associated with the probability of evolving resistance via mutations that provide escape from phage predation. The probability of resistance mutations enabling escape was predicted by sequence differences in tail structural genes between otherwise closely related lipopolysaccharide-binding phages. These short-term fitness differences of CRISPR-Cas immunity control longer-term dynamics of bacteria-phage communities with implications for phage therapy and understanding the role and distribution of CRISPR-Cas immunity in nature.

Professor Michael Brockhurst, University of Manchester, UK

Professor Michael Brockhurst, University of Manchester, UK

I am an evolutionary biologist based at University of Manchester. My lab uses experimental evolution to study the evolutionary dynamics of microbial genomes, populations and communities. We are especially interested in understanding the roles of horizontal gene transfer and mobile genetic elements in driving bacterial genome evolution. As well as lab-based experimental studies we also study microbial evolution in the field, including in human infection and natural environments.

Toxin-antitoxin (TA) systems are highly prevalent in bacteria, where they serve a variety of functions including phage defence. We have recently shown that the Bacillus subtilis homologue of the MazEF TA system is utilized by temperate phages of the SPbeta family for their communication-dependent lysis-lysogeny decision and that it can restrict the lysis of phage mutants lacking antitoxin gene homologues. Here, I will discuss the prevalence of this toxin-antitoxin system and of phages that utilize it and explore whether it serves its host as an antiphage system or is utilized for other means. Our results suggest that this TA system has a previously unappreciated and novel functional role, different from what has been previously proposed for MazEF or other TA systems.

Professor Avigdor Eldar, Tel Aviv University, Israel

Professor Avigdor Eldar, Tel Aviv University, Israel

The Eldar lab is studying microbial cooperation, conflict and communication. In recent years, the lab has shifted its focus to works on bacteria-phage conflict and on phage-phage interactions. Our main interest in that regard is the design principles of defense systems, with an emphasis on ‘altruistic’ (abortive infection) systems and on the lysis-lysogeny decision of temperate phages and its relation to phage communication and other interactions, to physiological information and anti-phage defense.

To this aim, the Eldar lab is combining experimental work which focuses on genetics, microscopy and conventional microbiology with theoretical work combining systems biology and evolutionary modelling approaches.

Immune defence mechanisms exist across the tree of life in such a wide diversity that the antiviral response of bacteria was considered unrelated to immunity of eukaryotes. Mechanisms of defence in divergent eukaryotes were similarly believed to be largely clade-specific.  However, recent data indicate that a subset of prokaryotic defence systems are conserved in eukaryotes and populate every stage of immune pathways. I will discuss the evolutionary dynamics of immunity across domains of life and how the conservation of immune modules can lead to discoveries in prokaryotes and eukaryotes. 

Dr Aude Bernheim, Institut Pasteur, France

Dr Aude Bernheim, Institut Pasteur, France

Aude Bernheim is a microbiologist interested in how bacteria fight off their viruses. She currently leads a lab at the Pasteur Institute in France exploring the conservation of immunity across domains of life. She's also an activist for a more inclusive and diverse science.