a14dedb4-65e8-48dc-a07b-be48d546a5df Siano Raffaele IFREMER 02 98 22 42 04 02 98 22 45 48 Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané Brest France Raffaele.Siano@ifremer.fr pointOfContact 2026-02-18T09:21:23.778993Z ISO 19115-3 - SEXTANT 1.0 0 WGS 84 (EPSG:4326) EPSG 8.6 Integrated eDNA and RNA-based monitoring of coastal microbiomes in French estuarine ecosystems, ROME project, 2020-2023 2020-09-01 creation 2021-05-21 publication FR-330-715-368-00032-IFR_BIOINFO_ROME DOI:10.12770/a14dedb4-65e8-48dc-a07b-be48d546a5df This study gathers multi-year environmental sequencing datasets generated within the French ROME pilot observatory network. It includes eDNA metabarcoding and RNA-based analyses from water samples, oyster tissues, and viral fractions collected across four French estuarine ecosystems between 2020 and 2023, supporting integrated monitoring of coastal microbiomes and microbial hazards. Ifremer (ROME consortium) IFREMER sismer@ifremer publisher Siano Raffaele IFREMER 02 98 22 42 04 02 98 22 45 48 Centre Bretagne - ZI de la Pointe du Diable - CS 10070 - 29280 Plouzané Brest France Raffaele.Siano@ifremer.fr author Serghine Joelle IFREMER PDG-DGDS-ODE-DYNECO-PELAGOS 02 98 22 43 63 Joelle.Serghine@ifremer.fr author Lebrun Luc IFREMER PDG-DGDS-ODE-COAST-LERBO 02 98 10 42 94 Luc.Lebrun@ifremer.fr author Terre Terrillon Aouregan IFREMER PDG-DGDS-ODE-COAST-LERBO 02 98 10 42 88 Aouregan.Terre.Terrillon@ifremer.fr author Chomerat Nicolas IFREMER PDG-DGDS-ODE-COAST-LERBO 02 98 10 42 91 Nicolas.Chomerat@ifremer.fr author Pepin Jean-Francois IFREMER PDG-DGDS-ODE-COAST-LERPC 05 46 76 26 20 Jean.Francois.Pepin@ifremer.fr author Seugnet Jean-Luc IFREMER PDG-DGDS-ODE-COAST-LERPC 05 46 76 26 25 Jean.Luc.Seugnet@ifremer.fr author Francoise Sylvaine IFREMER PDG-DGDS-ODE-COAST-LERN 02 31 51 56 35 Sylvaine.Francoise@ifremer.fr author Hernandez Farinas Tania IFREMER PDG-DGDS-ODE-COAST-LERN 02 31 51 56 17 Tania.Hernandez.Farinas@ifremer.fr author Normand Julien IFREMER PDG-DGDS-ODE-COAST-LERN 02 31 51 56 34 Julien.Normand@ifremer.fr author Parnaudeau Sylvain IFREMER PDG-DGDS-RBE-MASAE-LSEM 02 40 37 41 07 Sylvain.Parnaudeau@ifremer.fr author Le Guyader Soizick IFREMER PDG-DGDS-RBE-MASAE-LSEM 02 40 37 40 52 Soizick.Le.Guyader@ifremer.fr author Serais Ophelie IFREMER PDG-DGDS-ODE-COAST-LEROC 04 99 57 32 92 Ophelie.Serais@ifremer.fr author Gianaroli Camille IFREMER PDG-ODE-LITTORAL-LERLR Camille.Gianaroli@ifremer.fr author Felix Christine Université de Montpellier christine.felix@umontpellier.fr author Gobet Angelique IFREMER PDG-DGDS-RBE-MARBEC-LAAAS 04 99 57 32 50 Angelique.Gobet@ifremer.fr author Arzul Isabelle IFREMER PDG-DGDS-RBE-ASIM 05 46 76 26 47 Isabelle.Arzul@ifremer.fr author Morga Benjamin IFREMER PDG-DGDS-RBE-ASIM 05 46 76 26 49 Benjamin.Morga@ifremer.fr author Chevignon Germain IFREMER PDG-DGDS-RBE-ASIM 05 46 76 26 46 Germain.Chevignon@ifremer.fr author Jacquot Maude IFREMER PDG-DGDS-RBE-ASIM 05 46 76 26 82 Maude.Jacquot@ifremer.fr author Leroi Laura IFREMER PDG-DGDS-IRSI-SEBIMER 02 98 22 46 49 Laura.Leroi@ifremer.fr author Durand Patrick IFREMER PDG-DGDS-IRSI-SEBIMER 02 98 22 46 07 Patrick.Guido.Durand@ifremer.fr author Noel Cyril IFREMER PDG-DGDS-IRSI-SEBIMER 02 98 22 43 34 Cyril.Noel@ifremer.fr author Lemoine Maud IFREMER PDG-DGDS-ODE-COAST-LERMPL 02 40 37 41 49 Maud.Lemoine@ifremer.fr author Quere Julien IFREMER PDG-DGDS-ODE-DYNECO-PELAGOS 02 98 22 44 68 Julien.Quere@ifremer.fr author Schmitt Sophie IFREMER PDG-DGDS-ODE-DYNECO-PELAGOS 02 98 22 43 47 Sophie.Schmitt@ifremer.fr author https://sextant.ifremer.fr/geonetwork/srv/api/records/a14dedb4-65e8-48dc-a07b-be48d546a5df/attachments/BioinfoMarine.png Habitats and biotopes GEMET - INSPIRE themes, version 1.0 2018-07-27T14:39:48 publication 2018-07-27 publication geonetwork.thesaurus.external.theme.httpinspireeceuropaeutheme-theme /Biological Environment/Bioinformatics Thèmes Sextant 2025-12-09 publication geonetwork.thesaurus.local.theme.sextant-theme Variables ODATIS 2023-10-13 publication geonetwork.thesaurus.local.theme.odatis_variables Bioinformatics ODATIS aggregation parameters and Essential Variable names 2025-07-29 publication geonetwork.thesaurus.external.theme.NVS.OD1 Analysis data Type de jeux de donnée ODATIS 2025-12-09 publication geonetwork.thesaurus.local.theme.type_jeux_donnee Open Licence grid utf8 -5.7554 4.2661 41.599 50.40 2020-09-01 2025-12-31 /home/ref-bioinfo/ifremer/dyneco/rome NETWORK:LINK https://wwz.ifremer.fr/rome/ WWW:LINK https://doi.org/10.12770/a14dedb4-65e8-48dc-a07b-be48d546a5df DOI Digital Object Identifier (DOI) The ROME (Reseau d’Observatoires de Microbiologie Environnementale integree) project brings together a comprehensive set of environmental sequencing datasets generated between 2020 and 2023 across four major French estuarine ecosystems: the Bay of Brest, Marennes-Oléron, the Bay of Veys, and the Thau Lagoon. Developed within a One Health framework, the project aims to establish an integrated observatory network for monitoring coastal microbiomes and associated microbial risks relevant to ecosystem, aquaculture, and human health. The project combines complementary sampling matrices and molecular approaches, including: (i) eDNA metabarcoding of inshore and offshore surface waters to characterize bacterial and protist communities; (ii) 16S/18S rDNA metabarcoding of adult Pacific oyster (Magallana gigas) tissue,, which act as bio-integrators of local microbial diversity; and (iii) RNA-based analyses targeting viral fractions to explore the presence of human enteric viruses in estuarine waters and oyster tissues. Samples were collected following standardized protocols at regular temporal frequencies (biweekly for water, monthly for oysters) and processed using high-throughput sequencing technologies (Illumina MiSeq for metabarcoding and Illumina NovaSeq for viral metagenomics). The resulting datasets document spatial and temporal variability of coastal microbiomes under contrasting hydrological and anthropogenic influences, including river runoff and shellfish farming areas. By integrating environmental, host-associated, and viral datasets within a single framework, the ROME project provides a unified resource for studying estuarine microbial biodiversity, detecting potential pathogenic taxa, and supporting the development of standardized, long-term microbial monitoring tools for coastal environments.