Viruses as key reservoirs of antibiotic resistance genes in the environment

International audienceAntibiotic resistance is a rapidly growing health care problem globally and causes many illnesses and deaths. Bacteria can acquire antibiotic resistance genes (ARGs) by horizontal transfer mediated by mobile genetic elements, where the role of phages in their dissemination in natural environments has not yet been clearly resolved. From metagenomic studies, we showed that the mean proportion of predicted ARGs found in prophages (0-0.0028%) was lower than those present in the free viruses (0.001-0.1%). Beta-lactamase, from viruses in the swine gut, represented 0.10 % of the predicted genes. Overall, in the environment, the ARG distribution associated with viruses was strongly linked to human activity, and the low dN/dS ratio observed advocated for a negative selection of the ARGs harbored by the viruses. Our network approach showed that viruses were linked to putative pathogens (Enterobacterales and vibrionaceae) and were considered key vehicles in ARG transfer, similar to plasmids. Therefore, these ARGs could then be disseminated at larger temporal and spatial scales than those included in the bacterial genomes, allowing for time-delayed genetic exchanges

FAIRing Research Data to Live @AuBi Platform

International audienceHosted by the Mésocentre Clermont-Auvergne [1], the Auvergne Bioinformatique (AuBi) platform is member of the Institut Français de Bioinformatique (IFB) [2]. Around 15 labs contributes to AuBi activities with scientific questions related to health, microbes, agronomy and environment disciplines. Despite a high diversity a research questioning, data that are produced, processed and analyzed belongs to four main categories : sequences, images, qualitative and quantitative data and digital models. We aim at sharing expertise and knowledge in handling these kind of large-scale data with computing and storage facilities administrated at Mesocentre.An update of general services are presented here in terms of computing and storage as well as our prospects in the coming months. Recently opened services like jupyter notebooks and gitlab server for code tracking are keys points towards reproducible sciences. In addition, our concern about security and safety data storage guided us for proposing a new storage services accessible from any labs on our campus. Among services administrated for biologists and bioinformaticians are mature tools, an OMERO [3] server for data visualization and (meta)-data storage as well as the bio-analysis platform Galaxy [4]. In addition to the administration and technical support, we are contributing to scientific projects, such as the microservice web portal for the PlateForme d’Exploration du métabolisme. The project started a year ago and we are offering an infrastructure and our expertise in tool development to improve metabolomic annotation and analysis from a cloud infrastructure. In addition, through the IFB, we interact with FAIRChecker [5] development team to improve the FAIRness of our microservices web services. A poster to specifically detail the project has been submitted.Considering the data lifecycle, we are collaborating on 3 main IFB project. Firstly, one project initiated with the Projet-flash ANR machine-actionable DMP for Life Sciences (maDMP4LS) and the Institut de l’lnformation Scientifique et Technique (INIST) team ended up into the produce a web form connected to OPIDoR DMP, to help users to estimate project cost on the Mesocentre. Secondly, as part of the MuDiS4LS project, Data Stewart Wizard project was used to develop DMP dedicated to platforms: images produced and annotated on the CLermont Imagerie Confocal platform [6] as well as images stored and analyzed on omero.mesocentre.uca.fr. Thirdly, we contributed to the previously OpenLink project renamed as MadBot [7] offering a web portal orchestrating project information from data production to data publication with a view and link to where data are stored (Galaxy, OMERO, ...)To support users towards open science, FAIR principles and reproducibility, we are working together with the “Open Science Unit” and the IFB training team, investing in training sessions. Training are oriented toward best practices in using the Mesocenter infrastructures as well as raising awareness about the proper use of metadata while storing image data. We are also offering training sessions for bioinformaticians for best practices (FAIR-bioinfo) and for biologists with the Galaxy Training Network with topics of interest for the AuBi community.All our actions are Open Science oriented. This is challenging as actions have to be coordinated and in agreement with the University and research Institutes strategies, the Information Systems Management and the GDPR regulations, and considering diversity of research programs and various types of produced and stored data.AcknowledgementsINIST, maDMP4LS, IS1-MuDiS4LS and MadBot teamsReferences1.www.mesocentre.uca.fr2.www.france-bioinformatique.fr3.http://www.openmicroscopy.org/4.Afgan et al. (2018) https://doi.org/10.1093/nar/gky3795.Gaignard et al. (2023) https://doi.org/10.1186/s13326-023-00289-56.https://ressources.france-bioinformatique.fr/fr/plateformes/aubi7.https://www.france-bioinformatique.fr/science-ouverte

FAIRing Research Data to Live @AuBi Platform

International audienceHosted by the Mésocentre Clermont-Auvergne [1], the Auvergne Bioinformatique (AuBi) platform is member of the Institut Français de Bioinformatique (IFB) [2]. Around 15 labs contributes to AuBi activities with scientific questions related to health, microbes, agronomy and environment disciplines. Despite a high diversity a research questioning, data that are produced, processed and analyzed belongs to four main categories : sequences, images, qualitative and quantitative data and digital models. We aim at sharing expertise and knowledge in handling these kind of large-scale data with computing and storage facilities administrated at Mesocentre.An update of general services are presented here in terms of computing and storage as well as our prospects in the coming months. Recently opened services like jupyter notebooks and gitlab server for code tracking are keys points towards reproducible sciences. In addition, our concern about security and safety data storage guided us for proposing a new storage services accessible from any labs on our campus. Among services administrated for biologists and bioinformaticians are mature tools, an OMERO [3] server for data visualization and (meta)-data storage as well as the bio-analysis platform Galaxy [4]. In addition to the administration and technical support, we are contributing to scientific projects, such as the microservice web portal for the PlateForme d’Exploration du métabolisme. The project started a year ago and we are offering an infrastructure and our expertise in tool development to improve metabolomic annotation and analysis from a cloud infrastructure. In addition, through the IFB, we interact with FAIRChecker [5] development team to improve the FAIRness of our microservices web services. A poster to specifically detail the project has been submitted.Considering the data lifecycle, we are collaborating on 3 main IFB project. Firstly, one project initiated with the Projet-flash ANR machine-actionable DMP for Life Sciences (maDMP4LS) and the Institut de l’lnformation Scientifique et Technique (INIST) team ended up into the produce a web form connected to OPIDoR DMP, to help users to estimate project cost on the Mesocentre. Secondly, as part of the MuDiS4LS project, Data Stewart Wizard project was used to develop DMP dedicated to platforms: images produced and annotated on the CLermont Imagerie Confocal platform [6] as well as images stored and analyzed on omero.mesocentre.uca.fr. Thirdly, we contributed to the previously OpenLink project renamed as MadBot [7] offering a web portal orchestrating project information from data production to data publication with a view and link to where data are stored (Galaxy, OMERO, ...)To support users towards open science, FAIR principles and reproducibility, we are working together with the “Open Science Unit” and the IFB training team, investing in training sessions. Training are oriented toward best practices in using the Mesocenter infrastructures as well as raising awareness about the proper use of metadata while storing image data. We are also offering training sessions for bioinformaticians for best practices (FAIR-bioinfo) and for biologists with the Galaxy Training Network with topics of interest for the AuBi community.All our actions are Open Science oriented. This is challenging as actions have to be coordinated and in agreement with the University and research Institutes strategies, the Information Systems Management and the GDPR regulations, and considering diversity of research programs and various types of produced and stored data.AcknowledgementsINIST, maDMP4LS, IS1-MuDiS4LS and MadBot teamsReferences1.www.mesocentre.uca.fr2.www.france-bioinformatique.fr3.http://www.openmicroscopy.org/4.Afgan et al. (2018) https://doi.org/10.1093/nar/gky3795.Gaignard et al. (2023) https://doi.org/10.1186/s13326-023-00289-56.https://ressources.france-bioinformatique.fr/fr/plateformes/aubi7.https://www.france-bioinformatique.fr/science-ouverte

FAIRing Research Data to Live @AuBi Platform

International audienceHosted by the Mésocentre Clermont-Auvergne [1], the Auvergne Bioinformatique (AuBi) platform is member of the Institut Français de Bioinformatique (IFB) [2]. Around 15 labs contributes to AuBi activities with scientific questions related to health, microbes, agronomy and environment disciplines. Despite a high diversity a research questioning, data that are produced, processed and analyzed belongs to four main categories : sequences, images, qualitative and quantitative data and digital models. We aim at sharing expertise and knowledge in handling these kind of large-scale data with computing and storage facilities administrated at Mesocentre.An update of general services are presented here in terms of computing and storage as well as our prospects in the coming months. Recently opened services like jupyter notebooks and gitlab server for code tracking are keys points towards reproducible sciences. In addition, our concern about security and safety data storage guided us for proposing a new storage services accessible from any labs on our campus. Among services administrated for biologists and bioinformaticians are mature tools, an OMERO [3] server for data visualization and (meta)-data storage as well as the bio-analysis platform Galaxy [4]. In addition to the administration and technical support, we are contributing to scientific projects, such as the microservice web portal for the PlateForme d’Exploration du métabolisme. The project started a year ago and we are offering an infrastructure and our expertise in tool development to improve metabolomic annotation and analysis from a cloud infrastructure. In addition, through the IFB, we interact with FAIRChecker [5] development team to improve the FAIRness of our microservices web services. A poster to specifically detail the project has been submitted.Considering the data lifecycle, we are collaborating on 3 main IFB project. Firstly, one project initiated with the Projet-flash ANR machine-actionable DMP for Life Sciences (maDMP4LS) and the Institut de l’lnformation Scientifique et Technique (INIST) team ended up into the produce a web form connected to OPIDoR DMP, to help users to estimate project cost on the Mesocentre. Secondly, as part of the MuDiS4LS project, Data Stewart Wizard project was used to develop DMP dedicated to platforms: images produced and annotated on the CLermont Imagerie Confocal platform [6] as well as images stored and analyzed on omero.mesocentre.uca.fr. Thirdly, we contributed to the previously OpenLink project renamed as MadBot [7] offering a web portal orchestrating project information from data production to data publication with a view and link to where data are stored (Galaxy, OMERO, ...)To support users towards open science, FAIR principles and reproducibility, we are working together with the “Open Science Unit” and the IFB training team, investing in training sessions. Training are oriented toward best practices in using the Mesocenter infrastructures as well as raising awareness about the proper use of metadata while storing image data. We are also offering training sessions for bioinformaticians for best practices (FAIR-bioinfo) and for biologists with the Galaxy Training Network with topics of interest for the AuBi community.All our actions are Open Science oriented. This is challenging as actions have to be coordinated and in agreement with the University and research Institutes strategies, the Information Systems Management and the GDPR regulations, and considering diversity of research programs and various types of produced and stored data.AcknowledgementsINIST, maDMP4LS, IS1-MuDiS4LS and MadBot teamsReferences1.www.mesocentre.uca.fr2.www.france-bioinformatique.fr3.http://www.openmicroscopy.org/4.Afgan et al. (2018) https://doi.org/10.1093/nar/gky3795.Gaignard et al. (2023) https://doi.org/10.1186/s13326-023-00289-56.https://ressources.france-bioinformatique.fr/fr/plateformes/aubi7.https://www.france-bioinformatique.fr/science-ouverte