Food systems bring socio-ecological environments into our guts through farming, herding, foraging, processing, buying, cooking and eating practices, all shaped by the different contexts in which they take place. These food-related practices, shaped by the organization of society, socio-cultural practices, and ecologies, play a key role in shaping nutrient intake and the gut microbiome, affecting its capacity to harvest energy and nutrients from the food. As such, the human gut microbiome’s health depends on the health of food systems and environments, as reflected in the notions of Planetary Health and One Health. In the EATWELL project, we have developed an integrated approach to the study of food systems and how they shape our bodies, including microbiomes, in ways that are situated in local contexts to contribute to the sustainable food-systems-for-health agenda. We do so in a radical interdisciplinary way and deploy Bhutan as an informative, unique, and critical case, aiding precisely in teasing out the situated nature of human (micro)biologies as shaped through localized food systems and socio-ecological environments. EATWELL has consisted of two main phases: 1) anthropological phase: Examining the socio-cultural, political-economic and ecological aspects of food-related activities transforming natural resources into ingested items, 2) nutrition/microbiome phase: Studying how seasonal eating habits shape nutrient intake and the gut microbiome. Since the start of the project, we have been researching cultivation, cow and yak herding, foraging, buying, cooking, and eating. We have observed how these practices vary according to the seasons, general activities, everyday life and ritual events, traditional and biomedical practices, as well as gender, age, and the socio-ecological environment. In 2023, 2024, and 2025, the anthropologists on the team have conducted fieldwork studying food systems in 7 sites across Bhutan for comparative purposes. Our preliminary findings have shown a surprisingly large variation in food habits and systems across the sites owing to these different aspects. Simultaneously and based on these preliminary observations, we have designed and carried out a large part of the second phase of the project. It has consisted of two main parts carried out in 3 sites. In the first cross-sectional part, which ended in the beginning of August 2025, we collected around 525 stool samples, each combined with a dietary recall and a nutrition/microbiome survey where we predominantly inquire about food related activities that are known or hypothesized to affect nutrient intake and the gut microbiome. The participants were recruited from two remote areas—Laya and Nangkor—and urban food environments—in Paro, Thimphu, Punakha and Wangdue—where we sampled migrants coming from the former to observe long-term evolution over generations of nutrient intake and the gut microbiome when people migrate to a radically different food environment. The second longitudinal part is still ongoing among 60 participants and consists of the same method repeated up to 10 times per person for one year. This will enable us to observe seasonal and activity-related variations in nutrient intake and the gut microbiome. The methods in EATWELL are radically interdisciplinary, involving ethnography, dietary recalls, stool sample collection, nutrition/microbiome surveys, metagenomic shotgun sequencing and bioinformatics to determine associations between socio-cultural food practices, nutrient intake and the gut microbiome as they evolve throughout seasonal variation and long-term evolution through migration. The project has the following overall aim: Develop an integrated approach to food systems that consider its different parts and their intricate entanglement. For this, we aim to 1) demonstrate how nutrition and the gut microbiome are associated with socio-cultural practices, 2) critically assess the universalist and biased assumptions of a large set of biological, biomedical, and nutritional sciences which exert a dominant influence in current approaches to food systems, 3) establish a mutually enriching conversation between the Buddhist-informed Bhutanese approaches to environment, food systems and health through GNH, and the global approaches to sustainable food systems for health as well as One Health and Planetary Health, 4) develop a radical interdisciplinary study program of food systems which advances knowledge about the intricate interplay between society, environment, food, nutrition and gut microbiome such that a situated understanding of food systems and health can be developed in a culture-sensitive way, 5) craft an integrated model for food system development that unites concerns for environmental sustainability, culture sensitivity, nutritional adequacy, gut microbiome, and health by engaging stakeholders and relevant actors and end-users in Bhutan and that can be replicated and adapted in different contexts.