The fecal microbiota of lactating Holstein cows: A meta-analysis highlighting key microbial profiles and methodological challenges

In cattle, the digestive microbiota has been poorly studied outside the rumen, despite its recognized role in animal physiology, health, and production. This study aimed to provide a comprehensive meta-analysis of the fecal microbiota of lactating Holstein dairy cows. A systematic PubMed online search identified 28 articles meeting strict inclusion criteria, along with 2 recently published articles, yielding more than 2,000 samples. Raw sequencing data targeting the 16S rRNA gene (V3-V4 region) were obtained either from public repositories or directly from the authors. The core microbiota was identified as the most prevalent and shared taxa, comprising 21 microbiota families that accounted for 82% of the relative abundance. A multigroup analysis was performed to correct for the article of origin effect and successfully identified 3 microbiota profiles. The meta-analysis approach is a rigorous method that ensures the independence of research results from experimental conditions, thereby enhancing the reliability and generalizability of the findings.