HoloRuminant project - WP2 - contains errors - PLEASE DO NOT DOWNLOAD

WARNING: The FASTQ filenames in this project are currently incorrect. Do NOT use them for analysis. Corrected filenames will be provided in a separate submission (or contact the corresponding author). This study is part of the HoloRuminant project (https://holoruminant.eu/), which aims to investigate microbiome associations across multiple body sites in ruminants, including nasopharyngeal, rumen fluid, feces, and milk. By integrating metagenomic sequencing data from these biological compartments, the project seeks to enhance our understanding of microbial interactions and their potential influence on host health and productivity. As part of this initiative, samples were collected at SRUC from 100 dairy calves at multiple life stages: newborn, 1 week old, 3 weeks old, weaning, two weeks post-weaning, 8 months old, pre-mating, pre-calving, 30 days in milk (DIM), and 100 DIM. This dataset contributes to the broader HoloRuminant effort by providing longitudinal insights into microbiome dynamics across key developmental and physiological transitions in dairy cattle. Samples were also collected from milk of adult cows over two lactations to investigate the microbiome dynamics preceding the development (or absence) of mastitis.