Today's businesses form a highly interconnected network of companies, organisations, technologies, consumers, products and services. The concept of the Digital Business Ecosystem (DBE) has been come life in order to build an Internet-based environment in which businesses will be able to interact with each other more efficiently. In a Digital Ecosystem, a leadership structure is formed in order to be capable of responding to the dynamic needs of the environment. The agent in a Digital Ecosystem can both be a client and a server at the same time. With the same message, agents can simultaneously offer a service to others as a Server and request help as a Client. Industries may have their own systems but they are not yet business ecosystems. Digital ecosystems rely on a technological infrastructure to mediate the formalisation of knowledge in SME networks, the creation of software services, and different type of interactions between SMEs. There are many fields of application in the agro-food industry where interoperability of information system would be essential. Amongst others food tracking and tracing, logistics, SRM and CRM integration all need interoperability solution in a heterogeneous environment. Our prototypes can help in building these cooperative information systems.