In the field of environmental biotechnologies, meta-omics approaches enable to finely understand microbial communities acting as catalysts. They thereby offer the possibility to develop more cost-effective processes, through ecological engineering approaches or through the design of operational biomarkers. However, the variety of processes and operating conditions worldwide is very high. It is therefore difficult to extend the conclusions gained on one specific system: achieving a critical mass of data appears as a keyissue to extract relevant and robust information. It highlights the need for data collection and organization at a large scale. We present a new software tool developed to favor the collection, requesting and sharing of such data: DeepOmics is a data warehouse dedicated to environmental biotechnologies. Its main objective is to promote the sharing of meta-omics data and high quality associated metadata. Deep-omics is an n-tier web application: the user interface is a single page application built using the Angular framework (https://angular.io/). It accesses the data using a RESTful API. The latter is built with the Symfony framework (https://symfony.com/) and its API-platform extension (https://api-platform.com/); it connects the different server-side processes. Data are stored in a relational database (PostgreSQL, https://www.postgresql.org/) as well as in an indexation and search engine (open-source version of Elasticsearch, https://www.elastic.co/fr/community).. DeepOmics offers the possibility to upload, request and export 16S metabarcoding data from several environmental biotechnologies, together with many relevant associated metadata, especially regarding operating conditions and process design. Standard data formats (csv, biom, fastq, …) were preferentially selected. DeepOmics also enables the graphical monitoring of analytical data. In DeepOmics, each project coordinator manages the rights associated to its project data (e.g. private, public). A test server has been released, with restricted access. We plan to open a pilot version to a wider community in the near future. DeepOmics is a user-friendly tool which should help to take full advantage of next generation sequencing data and to turn knowledge into operational outputs. It will also promote the better agreement of the collected data with the FAIR data principles.