To ensure the usefulness of a bioinformatics service, analysis of user needs is an essential step. Furthermore, if the service anticipates the identified needs, acceptance by the user is easier. The aim of this work is to provide an overview of the requirements of a microbial diversity research community for ontology-based text-mining applications. This study is part of the development of the European infrastructure for text-mining, OpenMinTeD, that targets Biodiversity among other research fields. The requirement analysis was completed through targeted online surveys, interviews, focus group meetings and workshops. This work yields to a detailed up-to-date landscape of stakeholders (data provider, producer and consumer), their potential role and their expectations of general interest with respect to text-mining applications. We introduce a user-centered approach to focus on microbiologist end-user functional requirements, including application user interfaces. The resulting description of these needs guides OpenMinTeD current development to design and develop activities within text-mining projects for microbiology community.