Hub members Have many expertise, covering most of the fields in bioinformatics and biostatistics. You'll find below a non-exhaustive list of these expertise
Searched keyword : Shotgun metagenomics
Related people (2)
Emna has joined the C3BI in 2016 and worked actively in the IGDA platform doing research and education. Now, she is also part of the Viral Populations and Pathogenesis Unit (PVP).
Genome assemblySequence analysisProgram developmentData integrationRead mappingLIMSParallel computingGene predictionShotgun metagenomics
After a PhD in informatics on graph analysis (metabolic networks and sRNA-mRNA interaction graphs) at the LaBRI (Université de Bordeaux), I joined the DSIMB team (INTS) for a post-doc on structural modeling. Then, I performed a second post-doc at Metagenopolis – INRA Jouy-en-Josas, where I was initiated to the analysis of metagenomic data. I was recruited at the HUB in 2015, and since I pursue the development of methods dedicated to the treatment of metagenomic data by combining either the treatment of sequencing data, the statistics, the protein structural modeling and the graph analysis.
AlgorithmicsClusteringGenome assemblyGenomicsMetabolomicsModelingNon coding RNASequence analysisStructural bioinformaticsTargeted metagenomicsDatabaseGenome analysisBiostatisticsProgram developmentScientific computingDatabases and ontologiesExploratory data analysisData and text miningIllumina HiSeqComparative metagenomicsRead mappingIllumina MiSeqSequence homology analysisGene predictionMultidimensional data analysisSequencingShotgun metagenomics
- Regulation of nasopharyngeal microbiome in normal healthy individuals(James DI SANTO - Innate Immunity) - Pending
- Changes in cellular pathways during SARS-CoV-2 infection upon drug treatment(Bjoern MEYER - Viral Populations and Pathogenesis) - Pending
- Identification, structural and functional analyses of peptides from SARS-Cov2 binding with high affinity to MHC-E and impact on NK cell responses in SARS-Cov2 infection(Huot NICOLAS - HIV, Inflammation and Persistence) - Pending
Related projects (13)
Listeria monocytogenes is a gram positive facultative intracellular foodborne bacterium responsible for serious clinical manifestations including febrile gastroenteritis, meningitis, encephalitis and maternofetal infections in humans and livestock. Intestinal microbiota plays fundamental roles in the resistance to foodborne infections. Intestinal microbiota commensals protect against pathogens by direct antimicrobial activity through production of bacteriocins, competition for nutrients or binding sites, stimulation of epithelial barrier function, immunomodulation and inhibition of virulence factors expression in gastrointestinal pathogens. On the other side, pathogens have developed tools to avoid commensal-mediated resistance to colonization. Thus, the interplay between gut commensals and L. monocytogenes is critical for the infection and the development of the disease. We have identified a Listeria monocytogenes toxin which modifies the intestinal host microbiota and allows Listeria survival in the intestinal content to later invade the intestine and deeper organs.
The dramatic increase in bacterial resistance to antibiotics, particularly of Gram-negative bacteria, poses an immediate threat to our health system. The main driver of this trend is the impact that antibiotics, including b-lactams, exercise on intestinal commensal flora of humans and animals by selecting resistant strains. The intestinal microbiota, with its large spectrum of bacterial populations, density and diversity, can be considered the epicentre of the emergence of resistance. The presence of a large community of phages, bacteria’s viruses, called phageome, able of performing gene transfer between bacteria, raised the question of their role as a reservoir of genes entailing resistance. This project has two objectives (i) to study the role of human stools’s phages in the spread of antibiotic resistant genes with a selection pressure and (ii) to gain insights into the fundamental ecology and biology of phages in the human gut over a time series analysis.
We are comparing the bacterial communities of domestic and sylvatic breeding sites and midguts of Aedes aegypti collected in Gabon.
The gastrointestinal tract of humans is colonized by hundreds of microbial species, - bacteria, archaebacterial, fungi, protozoa and viruses -, collectively named the gut microbiome. The intestinal commensal bacteria have an important role in metabolic processes and contribute to colonization resistance against intestinal pathogens. Fungi are usually considered to be a minor component of the global microbiome. However, the mycobiome (fungal component of the entire microbiome) has been in fact little studied particularly with regards to its relationships with the other components of the microbiome. It seems however that fungi can be important players of the microbiome because some fungal species are able to proliferate in response to diet or during dysbiosis due to antibiotic treatment or gut inflammation. Consensus approaches to explore mycobiome together with other components of the mycobiome are still lacking. In this context the primary goal of our project will be to determine the best means to analyze bacterial and fungal microbiome concomitantly, using an identical technical procedure. We will evaluate the effectiveness of different methods for: 1) sample conservation; 2) DNA extraction; 3) mapping fungal and bacterial databases. The best procedure then will be used on samples from different studies to analyze interactions and respective dynamics of fungal and bacterial microbiome in different clinical settings.
A large fraction of diversity of the Archaea is still poorly explored. We are targeting environmental samples to extract genomic data of archaeal lineages of specific interest from an evolutionary point of view. We will probe available sequence data from public environmental metagenomics databases to identify specific lineages. In parallel, we will produce our own data from selected environmental samples containing these lineages. These data will allow filling up poorly explored branches of the tree of Archaea and bring important information on the metabolic diversity and adaptation to various environmental conditions, including the human microbiome.
Development of a bioinformatics workflow dedicated to the analysis of the viral metagenome: from NGS raw data to the identification of novel viruses
The aim of this project is to implement, at the level of the research units, a bioinformatics workflow dedicated to the analysis of the microbiome, and of the virome in particular, based on Next Generation Sequencing (NGS) data (Illumina technology). This workflow will be applied in different contexts, from the identification of nucleotide sequences belonging to a novel or emerging pathogen (mainly viruses) presente in a clinical sample (such as serum or cerebrospinal fluid), to the determination of the whole sequence genome of isolated and uncharacterized viruses (such as bacteriophages of Leptospira).
Environmental and human surveillance of polioviruses, VDPVs, and other enteroviruses in Madagascar during the switch from tOPV to bOPV
Poliomyelitis has been a major public health concern and currently, efforts are being made towards eradicating wild poliovirus type 2 (WPV2). A global switch from trivalent oral poliovirus vaccine (tOPV) to bivalent oral poliovirus vaccine (bOPV without PV2) is planned to take place this year in countries, like Madagascar, where epidemics of type 2 pathogenic circulating vaccine-derived polioviruses (cVDPVs) occur when low polio vaccine coverage allows the circulation and genetic drift of vaccine attenuated PV2 that can thus become pathogenic. In an attempt to monitor the presence and eventually absence of wild poliovirus 2, environmental and human surveillance will be conducted before, during, and after the switch in two regions in Madagascar. PV2, in particular cVDPVs and other enteroviruses will be genetically characterized. These data will support monitoring efforts and confirm the elimination of type 2 PV strains that have been implicated in outbreaks in this country.
16S OTU assignment and statistical analysis of zebrafish microbiota in different experimental conditions.
Identification of new or unexpected pathogens, including viruses, bacteria, fungi and parasites associated with acute or progressive diseases
Microbial discovery remains a challenging task for which there are a lot of unmet medical and public health needs. Deep sequencing has profoundly modified this field, which can be summarized in two questions : i) which pathogens or association of pathogens are associated with diseases of unknown etiology and ii) among microbes infecting animal (including arthropod) reservoirs, which ones are able to infect large vertebrates, including humans. We are currently addressing these two questions and our current request comes with the willingness for Institut Pasteur to increase its contribution and visibility of this thematic, in particular in relation with hospitals and the Institut Pasteur International network (IPIN). We expect to identify new microbes associated with human diseases, and this is expected to pave the way for basic research programs focusing on virulence mechanisms and host specificity, and will also lead to phylogenetic and epidemiological studies (frequency of host infection, mode of transmission etc...), as well as the development of improved diagnostic tests for human infections. Our objective is also to contribute to the efforts of Institut Pasteur in the field of infectious diseases, by building a pipeline, from sample to microbial identification, able to manage large cohorts of samples. This project is currently supported by the LABEX IBEID and the CITECH, and critically requires a bioIT support, justifying this application. Partners include different hospitals including Necker-Enfants malades University Hospital regarding patients with progressive disease, different IPIN laboratories, as well as INRA and CIRAD regarding animal/arthropod reservoirs.
As a part of BIRDY program (http://www.charliproject.org/), this project aims to study the microbiome composition and its dynamics in early infancy in Madagascar. It will provide genomic knowledge on antibiotic resistant strains and resistance genes circulating in this island. It will identify factors influencing the outgrowth of pathogenic bacteria, including ESBL-PE and decipher the role of the gut microbiome. The developed comprehensive modeling framework will be easily adaptable to other epidemiological questions related to the impact of any human intervention on the gut microbiome and of other environments such as skin, nose or urogenital tract. This project will contribute to the transfer of expertise in genomics and bioinformatics to the IP Madagascar partners.
Anopheles mosquitoes are the vectors of Plasmodium parasites, the etiological agents of malaria in humans. In Anopheles gambiae, a major vector in Africa, parasite transmission is largely under genetic control. We have previously shown that a gene family is implicated in the immune control of the parasite in this vector. The response of the family members is pathogen-specific, with one controlling P. falciparum infection and the other controlling rodent parasites. Recently, the genome of Anopheles stephensi, the major Asian vector, has been sequenced and, in this species, there is only one gene. Knocking down this gene reduced lifespan of A. stephensi and antibiotic treatment restores a normal longevity, suggesting the implication of the gut microbiota. Therefore, we conducted a metagenomic analysis in order to identify the bacteria responsible for the shorten of the mosquito lifespan.
Characterization of the bacterial and fungal microbiota in Aedes aegypti natural breeding sites and larvae
Although the microbiota of mosquitoes is known to play an important role in their vectorial capacity for human pathogens, most earlier studies have focused on mosquito-bacteria interactions at the adu