Understanding the role of the microbiota—the collection of microorganisms living in and on animals—is becoming increasingly important in livestock breeding. However, because these microbial communities are highly complex and influenced by many factors, studying their effects can be difficult. To help address this challenge, researchers developed a new software tool called HoloSimR, which allows scientists to simulate how animal genes and microbiota evolve together under breeding strategies. HoloSimR is an R package that helps researchers explore how the microbiota contributes to traits of interest in animals, such as health or productivity. It allows users to simulate different breeding scenarios, including how environment, host genetics, and microbial interactions influence outcomes. The tool is efficient, easy to use on standard computers, and can reproduce realistic microbial patterns using real data. By using HoloSimR, scientists can better understand which microbes are most influential, test hypotheses, and design improved breeding programs that take the microbiome into account. This helps pave the way for more sustainable and precise animal breeding methods that incorporate not just genetics, but the tissue-specific microbes living with the host.

Read the full article in the Journal of Animal Science.