The human body and its microbial communities form a ‘holobiont’ or ‘metaorganism’, which acts as a complex and synergistic entity. A disequilibrium in the microbiota component of the human ‘holobiont’ results in the pathogenesis or development of diseases. Microbiome research has revolutionised the field of molecular diagnosis and has introduced new avenues for development of therapeutic measures for the treatment of human diseases. Despite the significance of microbiomes in general and human health in specific, the current textbooks of science curricula in the Indian education system do not explicitly include the concept of ‘microbiomes’. Although efforts have been made to sensitize students about microbiomes in the curriculum framework; but lacunae still exist in the understanding and information related to microbes and microbiomes. To bridge this gap of understanding of the ecological, nutritional, and physiological interactions that shape the microbiomes, we have reviewed and addressed the need to introduce microbiome literacy in school education. We have discussed the importance of microbiomes of the eyes, ears, nose, and hair follicles and their consequences due to dysbiosis in human health and diseases. The objective of the present study was to evaluate and assess the importance of microbiome literacy at the school level. To achieve this objective, we identified the conceptual gaps in existing information documented in science textbooks for inclusion of microbiome literacy. We identified some core concepts or themes in NCERT Biology textbooks which can be extended to inculcate microbiome education. These topics include the understanding of health, hygiene, immunity, antibiotic resistance and environmental sustainability. We have also included some classroom exercises, which can be introduced for students to appreciate the microbiome studies. Thus, by introducing microbiome literacy in the school curriculum using pedagogical interventions, schoolchildren can be trained as educators and stimulants for societal health.