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Species diversity, and the various interactions that occur between species, supports ecosystems functioning and benefit human societies. Monitoring the response of species interactions to human alterations of the environment is thus crucial for preserving ecosystems. Ecological networks are now the standard method for representing and simultaneously analyzing all the interactions between species. However, deciphering such networks requires considerable time and resources to observe and sample the organisms, to identify them at the species level and to characterize their interactions. Next-generation sequencing (NGS) techniques, combined with network learning and modelling, can help alleviate these constraints. They are essential for observing cryptic interactions involving microbial species, as well as short-term interactions such as those between predator and prey. Here, we present three case studies …