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.