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Microbial Ecosystems

Dissecting microbial functions and communities to understand how microbes interact with their environments

Participants

Chairs

Rob’s  research focuses on developing computational methods for reconstructing genomes from metagenomic data, examining microbial diversity, and understanding the roles of microbes and their interactions within different ecosystems. His team has made significant contributions, such as defining a new blueprint for the human gut microbiome, developing tools like VIRify for identifying viral genomes, and creating the Skin Microbial Genome Collection (SMGC). He is responsible for the MGnify resource, which offers access to metagenomic, metatranscriptomic, and assembly analyses. This platform helps researchers study the functional and taxonomic profiles of microbial communities across various environments.

Nassos’ work bridges genomics, genetics, and high-throughput functional assays (biochemistry, cell biology) to explore bacterial cellular networks and their interactions with the environment, hosts, and other bacteria. Key areas of research include: i) the mechanisms by which antibiotics act within bacterial cells, how bacteria develop resistance and strategies to circumvent this resistance; ii) understanding the molecular interactions at the host-pathogen interface, particularly focusing on interactions between bacteria and their viruses, bacteriophages; and iii) the gut microbiome and understanding the role of interactions between its members and the environment in shaping and controlling community composition. The group has studied the impact of medication on gut bacteria, investigating the role of both antibiotic and non-antibiotic drugs can in gut community composition, and is now developing systematic genetic resources in gut bacteria to enable mechanistic and functional studies in the human gut microbiome.

EMBL Members

Her research focuses on the metabolic potential of gut bacteria and how these microbes adapt to various environments, particularly within the human host. Her  work integrates computational modelling with multi-omics data (including genomics, transcriptomics, proteomics, and metabolomics) to explore how gut bacteria respond to environmental changes, such as nutrient availability and medical treatments and to enhance the functional annotation of metabolic genes that are key to the microbiome. 

His research focuses on understanding the metabolic interactions between the gut microbiome and its host. Using a combination of high-throughput mass spectrometry, bacterial genetics, and computational models his team hopes to identify enzyme-encoding genes responsible for metabolising various compounds, including drugs, nutrients, and toxins. By developing mathematical models, they predict how these interactions affect drug metabolism and overall host health, with goals to enhance the functional annotation of microbiome data and understand microbiota contributions to drug toxicity.

His research focuses on the development and application of stability proteomics to study protein interactions and functions within cells. One of his significant contributions is the development of Thermal Proteome Profiling (TPP), a technology that enables the identification of drug targets on a proteome-wide scale in living cells. TPP assesses the thermal stability of proteins to infer their interactions with drugs, metabolites, and other proteins. This method has been pivotal in drug discovery and understanding the cellular impact of various treatments. 

image of John Lees

John Lees

Group Leader and Co-chair of Infection Biology Transversal Theme

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His research focuses on pathogen informatics and modelling, particularly in understanding the genomic epidemiology and evolution of bacterial pathogens. The Lees Group develops bioinformatics tools and mathematical models to analyse whole genome sequencing data, aiming to better control pathogen threats by studying genome evolution, transmission, and the impact of vaccines and antimicrobial resistance. Lees is committed to open-source software and data sharing, enhancing collaborative efforts in pathogen research.

Jordi van Gestel’s research explores the evolution of microbial development, particularly in the context of predation. The group uses an interdisciplinary approach that includes quantitative single-cell microscopy, microfluidics, functional genomics, high-content CRISPR libraries, experimental evolution, and mathematical modelling. His research studies into how predator-prey interactions among microbes, such as soil-dwelling Bacillus subtilis and Dictyostelium discoideum, influence their development and evolutionary strategies. These interactions can lead to complex behaviours and adaptations, including collective motility and resistance to predation, which are crucial for understanding broader ecological and evolutionary processes.

Her research focuses on the creation and enhancement of bioinformatics resources and tools for protein sequence and functional annotation. A central aspect of her work is overseeing the UniProt database, a comprehensive resource for protein information that is critical for scientific research globally. Martin’s team develops and maintains various tools, including those for the Gene Ontology (GO) Annotation and the Enzyme Portal, which aid in understanding protein functions and their biological roles.

The Bork group employs metagenomics to uncover microbial community principles underlying global microbiomes. The Tara Oceans Consortium explores marine microbiomes through oceanic expeditions, while soil microbiomes are studied via global and coastal sampling. Human microbiome research focuses on the gut, identifying three main gut microbial community types (enterotypes) and unique individual strains, with implications for health and disease diagnostics. His group also develops resources including functional annotation, visualisation, and global gene cataloguing.

The research led by Julio Saez Rodriguez group aims to gain a functional understanding of cellular network deregulation in diseases such as cancer, autoimmune disorders, and fibrosis, with a focus on developing novel therapeutics. By integrating big data (‘Omics’) with mechanistic molecular knowledge, his team constructs computational models tailored to understanding and treating diseases, collaborating closely with experimental groups. With a particular interest in cancer and fibrosis, they develop open-source computational tools and support scientific crowdsourcing through collaborative competitions like the DREAM challenges. The group operates across two sites: EMBL-EBI and Heidelberg University.

The Vincent group investigates the diversity and ecological impact of marine microbial interactions, particularly focusing on symbiosis within unicellular eukaryotes like phytoplankton. In collaboration with the Tara Ocean’s expedition, her team’s research combines single-cell isolation, genotyping, and imaging to uncover symbiotic relationships, such as those between diatoms and ciliates, and their effects on carbon cycling and microbial communities. The aim is to enhance our understanding of marine symbioses and their crucial role in maintaining ecosystem processes.

Maria Garcia Alai’s group focuses on developing systematic pipelines of biophysical techniques to address dynamic structural questions. Her team’s integrated structural biology approach investigates the mechanisms of assembly and disassembly of transient protein-lipid complexes, and in particular focusing on protein-lipid interactions that are key for endocytosis and cellular trafficking. Maria also is the head of the high-throughout crystallisation facility at EMBL.

Georg Zeller’s team focuses on developing analysis strategies and tools to understand the role of the human microbiome in health, disease progression, and treatment outcomes, and how it’s influenced by host factors like nutrition and medication. Their efforts involve developing software tools for precise microbial profiling, employing statistical and machine learning approaches to associate changes in microbiome profiles with host phenotypes, and establishing diagnostic microbiome signatures, particularly in colorectal cancer. The Zeller group is now based at based at Leiden University Medical Center  in the Netherlands.

The group led by Zamin Iqbal operates at the intersection of bioinformatics and microbiology, focusing on developing algorithms for pan-genome graphs and sequence and image analysis for studying drug resistance in Mycobacterium tuberculosis. His team’s research includes the evolution of plasmids and global TB surveillance. Additionally, the team has pioneered techniques for searching bacterial and viral genomic data and analysing transposon and plasmid evolution. The group is transitioning to the University of Bath.

External collaborators

Lisa Maier

Professor, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen (Germany)

The Maier group focuses on the interactions between the human microbiome and its host, exploring how microbial lifestyles influence health. Her lab employs interdisciplinary methods at the nexus of microbiology, systems biology, and computational biology. Key areas of interest include drug-microbiome-host interactions, microbial colonisation dynamics, and microbiome modulation, with an overarching goal of translating their findings into clinical applications to enhance human health. She is currently coordinating the German Research Foundation (DFG) funds new Priority Programme “Decoding new gene functions in the human gut microbiome”.

Andre Mateus

Assistant professor at University of Umeå and the Laboratory of Molecular Infection Medicine (Sweden)

 

Research in the Mateus group focuses on understanding protein functions and interactions within the human gut microbiome using proteomics and systems biology approaches. The aim is to map and modulate these protein functions to promote a healthy gut microbiome. His work involves using drugs and genetic manipulation followed by a proteome measurement, helping to elucidate drug mechanisms of action and resistance. Additionally, the Mateus group seeks to understand nutrient metabolism within gut microbiome species and their community interactions, ultimately aiming to develop strategies to maintain or restore healthy microbiome compositions.

Kiran Patil

Professor of Molecular Systems Biology, MRC Toxicology Unit, University of Cambridge (UK)

The Patil Group investigates the interactions between the microbiome and various xenobiotics, including drugs and pollutants. Their research aims to understand how these interactions contribute to  drug efficacy, side effects, and toxicity. They use a combination of computational modelling, bioinformatics, machine learning, and experimental techniques such as microbiomics and metabolomics to explore the complex metabolic networks in the gut microbiota.

Joel Selkrig

University Junior Professor for Mucosal Infection Biology, University of Aachen (Germany)

Research in the Selkrig group focuses on understanding how protein secretion by commensal gut bacteria influences human health and disease. Utilising advanced proteomics, his work aims to uncover effector proteins secreted by these bacteria, elucidating their roles in host interactions and pathogenesis. This research holds significant potential for developing new therapeutic strategies and enhancing our understanding of host-microbe interaction. 

Alexander Westermann

Professor, Chair of Microbiology, Biocenter, University of Würzburg & Group Leader, Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg (Germany)

The Westermann group maps the complex network of interactions between the intestinal microbiota, the host and the invading pathogens during the infection process. Their research seeks to identify and functionally characterise noncoding RNA molecules and RNA binding proteins of human gut microbes and enteropathogens to advance the development of targeted RNA-based diagnostics and therapeutics.

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