A holobiont is defined as a meta-organism consisting of a host (e.g., animal, plant, alga) and its associated microbiota. A healthy holobiont is considered to have a resilient microbiota, which may adapt and respond differently depending on external disturbances . The importance of the holobiont concept is increasingly coming into the focus of ecological and clinical research due to the major role of, for instance, digestive microbiota in host digestion, host health, and host development [2–5]. For instance, the ruminant gastro-intestinal tract contains specific bacterial groups able to degrade complex plant cell-wall polysaccharides such as cellulose, hemicelluloses, and pectins, allowing polymer assimilation during digestion and accounting for 70% of the host energy intake .