A multi‑kingdom metabarcoding study on cattle grazing Alpine pastures discloses intra‑seasonal shifts in plant selection and faecal microbiota

Diet selection by grazing livestock may affect animal performance as well as the biodiversity of grazed areas. Recent DNA barcoding techniques allow to assess dietary plant composition in faecal samples, which may be additionally integrated by the description of gut microbiota. In this next generation sequencing-based metabarcoding study, we investigated the diversity of plant, fungal and bacterial taxa in faecal samples of lactating cows of two breeds grazing an Alpine semi-natural grassland during summer. The estimated plant composition of the diet comprised 67 genera and 39 species, which varied remarkably during summer, suggesting a decline of the diet forage value with the advancing of the vegetative season. The fungal community comprised Neocallimastigomycota gut symbionts, but also Ascomycota and Basidiomycota plant parasite and coprophilous taxa, likely ingested during grazing. The proportion of ingested fungi was remarkably higher than in other studies, and varied during summer, although less than observed for plants. Some variation related to breed was also detected. The gut bacterial taxa remained stable through the summer but displayed a breed-specific composition. This study offered insights in the reciprocal organisms’ interactions affecting, and being affected by, the foraging behaviour: the flowering higher eukaryotes showed a high temporal variation, the cryptogamous lower eukaryotes a smaller temporal variation, and the asexual prokaryotic unicellular biota no temporal variation; conversely, the three kingdoms showed the opposite gradient of variation as respect to the animal host breed, as the organisms of lowest complexity revealed to be the ones mostly characterized by host-specificity.