Transcriptomic and 16S rRNA amplicon sequencing of colonic mucosa and microbiota in Mycoplasma ovipneumoniae-infected goats: comparison of commercial and self-made vaccine vaccine protection

This BioProject contains high-throughput sequencing data from a goat model investigating the impact of Mycoplasma ovipneumoniae (Mo) infection on distal intestinal (colonic) homeostasis via the lung-gut axis, and the protective effects of a commercial inactivated vaccine (CV) versus a self-developed vaccine (SV).Eighteen Mo-negative goats were divided into four groups (control, Mo-infected, CV-vaccinated + Mo-challenged, SV-vaccinated + Mo-challenged). Animals were vaccinated on Day 0, intratracheally challenged with Mo on Day 28, and euthanized on Day 56 for sample collection.Colonic mucosal samples were subjected to poly(A)-enriched RNA sequencing (Illumina NovaSeq 6000) to characterize host transcriptomic responses, including differential gene expression and KEGG pathway enrichment related to immune remodeling, mucus secretion, antigen presentation, and epithelial transport.Colonic luminal contents were used for 16S rRNA gene amplicon sequencing (V3-V4 region, Illumina MiSeq PE300) to profile microbial community structure, diversity, and taxonomic composition, revealing Mo-associated dysbiosis (e.g., Akkermansia expansion) and vaccine-mediated restoration of SCFA-producing taxa.Integrated host-microbiota analyses explored correlations between microbial modules and epithelial immune/barrier gene networks. These datasets provide insights into vaccine-mediated restoration of mucosal homeostasis during respiratory mycoplasma infection in small ruminants.Raw sequencing reads are deposited in the Sequence Read Archive (SRA), linked to this BioProject.