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Origins and dynamics of oral dysbiosis associated with environmental enteric dysfunction. Preventive intervention in Central African infants. Objectives and research hypothesis Considering that the presence of oropharyngeal pathobionts in the duodenum and the gut […]

The popCell project aims to characterize the variation in immune response to SARS-CoV-2 of peripheral blood mononuclear cells (PBMCs) from > 200 adult, healthy volunteers of West European, Central African and East Asian origin, […]

Bacteria face many unexpected challenges, which require responses that may be difficult to prepare. This is often the case of antagonistic biotic interactions, e.g. when phages infect bacteria, which are regulated by evolutionary processes […]

The ability of an organism to interact with its environment is an essential part of life at the cellular, organismal and species levels. In many cases, rapid cellular adaptation involves modifications to chromatin, which […]

Decoding the genetics of menstruation evolution in primates The shedding of the superficial endometrium (menstruation) is a recent evolutionary attribute. It occurs only in few placental mammals (including humans and baboons), when in most […]

In nature, cells alternate between replicative and non-replicative states depending on the fluctuating environmental conditions and physiological requirements (Koch, 1971). The non-replicative state resulting from cell division arrest or transition to a more specialized […]

Pathogenic Leptospira lack many classical virulence factors and approximately 35% of their genome encode proteins of unknown function. Their virulence mechanisms and how they subvert the host and colonize tissues remain largely unknown. To […]

Bacteria exchange and recombine DNA to accelerate their evolution and adapt to new stress. Their evolvability is illustrated by the rapid emergence of multi resistant bacteria after the introduction of antibiotics. The most powerful […]

Between 2018 and 2022, and as Biomics project manager, I contributed to a large capacity building in Pathogen-Host Interaction Data access project (PHINDaccess) which is coordinated by the Institut Pasteur de Tunis (IPT) and […]

Vector-borne pathogens like dengue or Zika viruses are transmitted to a human via the bite of a mosquito infected by a previous bite on an infected human. This transmission cycle is responsible for the […]

The emergence of new resistant bacterial strains is a worldwide challenge. A resistant bacterial population can emerge from a single cell that acquires resistance or persistence. Hence, new ways of tackling the mechanism of […]

Antimicrobial resistance (AMR) is a major global health issue and development threat. Profound knowledge of the mechanisms employed by bacteria to defend themselves under antibiotic selective pressure is critical to controlling the rise and […]

We are interested in identifying host genetic factors affecting the susceptibility of mice to infection by SARS-CoV-2 using Collaborative Cross (CC) mice. Since mice were not naturally susceptible to the first (Wuhan) strains of […]

Free-living bacteria commonly cope with and adapt to changing environments. We have shown that various families of antibiotics are capable, at concentrations as low as 1% of the MIC, to activate stress responses in […]

The RepliChroms project aims at decrypting plasmid adaptation mechanisms in their bacterial host. Bacterial genomes are composed of two types of replicons: chromosomes and plasmids. Bacteria commonly have a unique circular chromosome, and current […]

During infection, Leptospira are confronted with dramatic adverse environmental changes such as deadly reactive oxygen species (ROS). Withstanding ROS produced by the host cells is an important strategy evolved by pathogenic Leptospira for colonizing […]

Retracing the global spread of Yersinia enterocolitica & the evolution of pathogenicity within its lineages, from a One Health perspective Abstract:The Yersinia species are instrumental models to investigate the emergence of pathogenicity in the […]

About the Nanopore User Group: The Nanopore User Group at Institut Pasteur was established in 2019 with the primary goal of fostering collaboration, sharing knowledge, and advancing the application of Oxford Nanopore Technologies (ONT) […]

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Sorry, this entry is only available in FR.

Bacterial genomes are mainly composed of two types of replicons: chromosomes and plasmids. Plasmids are accessory mobile genetic elements acquired by horizontal transfer between strains or species. Their domestication by new hosts is of […]

Towards the design of new nitrogen fixing symbionts Elucidate how the capacity to establish a nitrogen fixing symbiosis with legumes has been acquired by new bacterial taxons via a lab-evolution experiment should allow developping […]

The Institut Pasteur has voluminous activities of microbial strain characterisation, in the context of epidemiological surveillance, biological resource centres collections management, and research. These activities involve National Reference Centers, WHO-collaborative centers, biological resources centers […]

This project aims to provide users of Biomics core facility with simplified protocols. The protocols are available in English and French. They include all the steps needed for sequencing: quantification, quality control, fragmentation, library […]

Clostridium difficile (CD), recently reclassified as Clostridioides difficile, a Gram-positive spore-forming anaerobic bacterium, has rapidly emerged as the leading cause of antibiotic-associated diarrheal disease in hospitals worldwide. The incidence and severity of CD infections […]

Although mouse models have been invaluable to study human diseases, classical mouse laboratory strains (figure, left panel, colored dots) present much smaller genetic diversity than the human population, limiting the range of phenotypic variations […]

Cellular mRNAs are subjected to a balance between synthesis and degradation, which determines the shape of the transcriptome and greatly participates to protein homeostasis. In addition to the general degradation pathways, which ensure the […]

In collaboration with the Institute of Vertebrate Biology in Brno, Czech Republic (Dr. Natalia Martinkova and Markéta Harazim), the aim of this project is to study the mechanisms of lyssavirus infection in bats based […]

The evolutionary roles of repeats Stress is often faced in nature, whether from lack of nutrients, arrival of competitors or predators, or the presence of toxic substances. The survival of stressed organisms can be […]

Endometriosis is a chronic gynecologic disease that occurs when endometrial tissue, which normally lines the inside of the uterus, grows outside of the uterine cavity. Endometriosis is thought to develop when endometrial fragments contained […]

Microbes have played fundamental roles throughout our evolution and history. These roles were not only played by pathogens, but also by the trillions of microorganisms inhabiting our body –the microbiome–, which are essential for […]

Ce projet vise à comprendre les interactions fonctionnelles et mécaniques entre chromosomes, périphérie nucléaire et cytosquelette, ainsi que leur influence sur la stabilité génomique, à travers des approches in vivo et in vitro chez […]

Human Evolutionary Immunogenomics: population genetic variation in immune responses Recent genome-wide association studies have successfully identified rare and common variants that correlate with complex traits. However, they have provided us with little insight into […]

Prokaryotes evolve rapidly new functionalities by horizontal gene transfer delivered by mobile genetic elements (MGE). MGE increase relatedness between individuals and thereby might also promote the establishment of microbial social networks. Many studies have […]

The folding of eukaryotic and prokaryotic chromosomes consists of an assortment of intertwined structural features. The resulting complex networks of contacts is highly dynamic and interacts functionally with, or regulates metabolic processes ranging from […]

Inferences concerning the action of selection provide a powerful tool for predicting regions of the genome associated with disease. As infectious diseases exert strong selection pressures, the identification of immunity-related genes targeted by selection […]

Evolutionary processes largely rely on the production of diversity. Genetic robustness, by allowing the accumulation of neutral diversity within a population, has been associated with increase in evolutionary potential (evolvability). We have already shown […]

By integrating cutting-edge knowledge and technology in the fields of genomics, population genetics, immunology and bioinformatics, our aim is to establish a thorough understanding of how variable the human immune response is in the […]

Salmonella enterica infections in humans are responsible for three major clinical syndromes, typhoid fever caused by host-specific Salmonella, a diarrheal disease known as salmonellosis caused by several non-typhoidal Salmonella (NTS) and invasive NTS (iNTS) […]

Zika virus is an arbovirus responsible for recent epidemics in Polynesia and in the Americas. Clinical descriptions range from mild flu-like syndromes to rare but severe neurological complications such as Guillain-Barré syndrome and encephalitis […]

Neurolisteriosis is a common and frequently fatal complication of Listeria monocytogenes infection in human and ruminants. It has a high impact on human and animal health, but only little is known about its pathogenesis. […]

The most important cultural innovation witnessed by modern humans has probably been the transition from a hunter-gatherer nomadic mode of subsistence to an agricultural sedentary lifestyle. This transition occurred in many parts of the […]

HIV-1 potent human broadly SARS-CoV-2 neutralizing IgA and IgG antibodies effective against omicron BA.1 and BA.2 Memory B-cell and antibody responses to the SARS-CoV-2 spike protein contribute to long-term immune protection against severe COVID-19, […]

The vast majority of the studies evaluate effects of the above-minimal inhibitory concentration (above-MIC) of antibiotics on bacteria. However, bacteria frequently encounter low concentrations of antibiotics in their environments. Our goal is to elucidate […]

We are studying different aspects of this gene capture system: their distribution, their contribution to the adaptive capacity of their host and their recombination processes. This natural genetic system is composed of two basic […]

The Oncobiomics project is conducted in the THE (heterogenity tumor ecosystem) national program launched by the cancer nation institute (Inca) in the third national cancer plan 2014-2019. It’s a consortium project involving 8 teams […]

The LISTERIAGEN project aims to identify host genetic factors associated with susceptibility to listeriosis.

The Oncobiomics project is conducted in the HTE (heterogenity tumor ecosystem) national program launched by the cancer nation institute (Inca) in the third national cancer plan 2014-2019. It’s a consortium project involving 8 teams […]

NovaSeq 6000 High throughput NGS sequencing is now available at Biomics core facility. This is using the same types of libraries as other Illumina sequencers. Sequencing (only PE150, ≥ 400M reads) is outsourced to […]

Rift Valley fever (RVF) is a an arthropod-borne emerging viral disease that primarily affects domesticated animals (such as cattle, sheep and goats) and humans, with recent outbreaks in sub-Saharan Africa, Madagascar, and the Arabian […]

Clostridium difficile is increasingly associated with infections in hospitals and in the community, and hypervirulent types are emerging. Six research groups from 5 countries undertook this project, aiming to use genomic approaches to study […]

PHINDaccess is a twinning initiative aimed to serve as a lever for Omics research performance of the Institut Pasteur de Tunis (IPT), aspiring to raise its positioning as an excellence center in the field […]

This third project is to investigate other factors involved in genome plasticity of the complex genome of Vibrio species. The Vibrio group includes a large number of pathogenic species whose hosts range from human […]

Gene expression is controlled and regulated by nuclear and cytoplasmic surveillance mechanisms in order to preserve the integrity of genetic information. Some of the mechanisms occur in the nucleus during transcription and maturation of […]

Knowledge concerning the interaction of SARS-CoV-2 with human and bat cells is sparse. We will use state-of-the-art RNA-sequencing analysis, original bioinformatics tools, loss-of-function approaches and mechanistic studies to identify and characterize coding and non-coding […]

Supervision of the quality management system (QMS) based on International Standards of Organization ISO9001 requirements is one of Biomics’ missions. The platform has been certified since 2017. An external audit system allows us to […]

The wide range of phenotypic variation in human populations may reflect distinctive processes of selection/adaptation to variable environmental conditions (e.g. climate, pathogens, nutritional resources). The advent of genome-wide datasets allows testing different hypotheses concerning […]

Replication-associated gene dosage effects Maximal growth rates are central to microbial life-history strategies because there is a trade-off between fast growth in copiotrophs and scavenging potential in slow-growing oligotrophs. When E. coli’s generation time […]

Translation involves four main steps: initiation, elongation, termination and recycling. Each step is highly controlled and can be modulated depending on the mRNA characteristics. The first step begins with the binding of eIF3 to […]