The importance of microbiome research is rapidly gaining momentum for understanding its role in development, evolution, ecology, health and disease. Recent progress in community and single-cell genomic approaches has provided an unprecedented amount of information on the abundance and ecology of microbes in different host organisms and turned them into metaorganisms. A metaorganism is a host and its complete microbial community which is commonly referred to as the microbiome. Over half the cells in a human body are not human but belong to the multitude of species that compose our microbiome. However, linkages between metaorganisms from different taxa and their in situ level of intraspecific dependence (be it growth, division or metabolic activity) are much more scarce. Visualization therefore is crucial for understanding host–microbe interactions as well as overarching concepts in different host organisms. Here we introduce an innovative user-friendly method for interactive visualization of microbiome multi-omics data. The new communication format combines science and visual communication design. Interactive media are used to transform scientific findings on host–microbe interactions in an intuitive way. The method provides access to additional layers of information that cannot be visualized using a traditional platform. We demonstrate the usefulness of this visualization approach using the interactive scientific poster ‘Digital Meta’, which is designed to support not only interdisciplinary co-working but also communication with the general public.