This project utilizes the attention on microbes that emerged during the design of a new microbial daycare in Tampere. The microbial daycare is a response to our collaborators’ research demonstrating that children’s weak interaction with environmental microbes in urban environments is linked to an imbalance in immune regulation. We introduce a new understanding of the child’s body as a ‘nested ecosystem’ highlighting its constitution by and connectedness with diverse microbes in the environment. We seek, first, to understand the complex perceptions about and relations between humans and microbes in daycare education. Second, we foster new pedagogical attention and practices that consider children’s diverse biology beyond the current focus on children’s social life. We make the microbes visible and relatable through a participatory metagenomics led by an ecologist with teachers and children. We also use arts to develop participants’ sensory perspective on microbes to be able to think, feel and sense the world from a microbial view. The pedagogical stories, scientific article and artworks created through these engagements communicate to scholars, professionals and the public that human life and health are connected to thriving biodiverse environments hence fostering those is a key to human wellbeing. Pedagogical encounters seek to promote ethical relations with and foster microbial diversity, an area still unrecognized in conservation yet plays a crucial role in changes to ecosystems.