Host Filtering Shapes the Soil–gut Microbiome Linkages in Pastoral Systems

Soil and ruminant gut microbiomes are linked within grazing pastoral systems, yet the strength and direction of these connections under different pasture management systems remain poorly understood. This study characterised bacterial communities in soil and faeces from cattle and sheep grazing standard and diverse pastures managed under contemporary and regenerative practices using 16 S rRNA gene sequencing. Shared bacterial taxa between soil and gut were identified, and their dominance patterns and soil-gut diversity relationships were evaluated using Spearman correlations and Procrustes analyses. Several taxa, including Prevotella copri, Faecalibacterium prausnitzii, Akkermansia muciniphila, Bacteroides uniformis, Clostridium perfringens and Fibrobacter succinogenes were commonly shared between soil and gut but were usually more prevalent in the gut, indicating predominant host‑associated dominance. Soil exhibited significantly greater bacterial alpha diversity than the gut across all treatments, and neither pasture diversity nor management significantly affected soil-gut alpha diversity differences or the contributions of shared taxa. Correlations between soil and gut alpha diversity were weak and non-significant, and correlations for beta diversity between soil and gut varied through time and among treatments without reaching significance. These findings indicate that, although soil-gut microbial connectivity exists, gut communities are primarily shaped by host-related ecological processes and internal filtering, with soil acting mainly as a diverse reservoir and sink for gut-derived taxa. This highlights that host-driven gut microbiomes primarily shape the soil-gut microbiome link, limiting the strong direct influence of pasture diversity or management.