Code for raw read processing using Qiime2

This is the code used in data processing and analysis in QIIME2 for manuscript “A randomized clinical trial to examine hazelnut skin extract’s effects on diarrhea and bronchopneumonia incidence, growth rate, antioxidant status, and fecal microbiota in neonatal dairy heifers”. This study investigated the potential of hazelnut skin extract (HS)—a polyphenol-rich by-product of the food industry—as a natural supplement aimed at enhancing health and reducing the incidence of disease in newborn dairy calves. A randomized clinical trial was conducted to assess the effects of early-life HS supplementation on the occurrence of neonatal diarrhea and respiratory diseases, as well as its influence on growth, oxidative status, and gut microbiota. The findings of this study provide valuable insights into the potential future application of these polyphenol-rich waste compounds in promoting sustainable livestock management.