Between November 2021 and March 2022, tracheobronchial lavage (TBL) samples were collected from 200 pre-weaned calves across 20 large dairy farms. Based on clinical assessments, TBL, fecal, and blood samples were collected from both healthy and symptomatic calves on each farm. The TBL samples were analyzed for viral and bacterial presence, while fecal samples were sequenced for bacterial communities. Blood samples were tested for acute phase proteins and cytokines. The study aims to understand the role of the respiratory microbiome in inflammation and disease, and to evaluate the impact of fecal microbiota in both healthy and diseased calves.