Seasonal dynamics in sheep fecal microbiome and soil bacterial communities under grazing management

The gut microbiome plays a key role in animal health, productivity, and environmental sustainability. As it represents a valuable proxy for animal welfare, its investigation has become increasingly important in livestock studies. With the growing focus on promoting sustainable livestock, supporting rural areas at risk of abandonment is receiving particular attention. Indeed, sheep grazing offers a promising strategy for improving sustainability, biodiversity, and land management. This study focuses on the interconnected dynamics between the sheep gut and soil microbiomes, assessing how seasonal changes and grazing activity shape microbial diversity and community structure across the animal-soil interface. Fecal and soil samples were collected throughout 2024 in a commercial farm in Tuscany, Italy: 215 fecal and 46 soil samples (23 pasture and 23 meadow - i.e., not grazed) were stored. Alpha and Beta diversity were assessed using the Kruskal-Wallis test and PERMANOVA, respectively, and the differential abundance analysis was also performed. The relative abundance analysis at the family and genus level revealed an increase in the number of taxa from winter to autumn in both fecal and soil samples. When the Chao1 index was considered, alpha diversity was higher in fecal samples, followed by soils. Principal Coordinate Analysis revealed distinct clustering between animal and soil microbiota, with slightly reduced differentiation in Summer. In fecal samples, the five most abundant bacterial families were Ruminococcaceae, Spirochaetaceae, Porphyromonadaceae, Lachnospiraceae, and Rikenellaceae, whose abundance varied seasonally. Ruminococcaceae, Lachnospiraceae, and Rikenellaceae decreased in Summer, while Spirochaetaceae and Porphyromonadaceae increased. The increased abundance of these families during Summer may reflect heat stress in animals. Differential abundance analysis also suggested potential microbial transfer from animals to soil: Peptostreptococcaceae and Erysipelotrichaceae were enriched in grazed soils across multiple seasons. Repeated cross-sectional studies like this are essential for understanding microbiome dynamics and animal-soil interactions in grazing systems.