Exploring the impact of grazing on fecal and soil microbiome dynamics in small ruminants in organic crop-livestock integration systems

• DOI: 10.1371/journal.pone.0316616
• Publication Date: 2025-01-17T20:03:24Z
• Authors: Sejin Cheong; Kimberly Aguirre-...; Sequoia R. Williams; Amélie C. M. Gaudin; Paulo Pagliari; Michele T. Jay-Ru...; Roselle Busch; Elizabeth A. Maga; Alda F. A. Pires
• Keywords: 570; Agricultural; Organic Agriculture; Sheep; Livestock; Shiga-Toxigenic Escherichia coli; Goats; Microbiota; Minnesota; Science; Q; R; Crops; 630; California; Feces; Soil; Escherichia coli; Animals; Medicine; Herbivory; Soil Microbiology; Research Article

In integrated crop-livestock systems, livestock graze on cover crops and deposit raw manure onto fields to improve soil health fertility. However, enteric pathogens shed by grazing animals may be associated with foodborne pathogen contamination of produce influenced fecal-soil microbial interactions. We analyzed 300 fecal samples (148 from sheep 152 goats) 415 (272 California 143 Minnesota) investigate the effects presence non-O157 Shiga toxin-producing Escherichia coli (STEC) or generic E . (gEc) in microbiomes. collected field trials three treatments (fallow, a crop without (non-graze CC), (graze CC)) grazed goats between 2020 2022. No significant differences STEC prevalence were found pre- post-grazing either goats. gEc was more prevalent CC soils compared fallow non-graze soils. Alpha diversity species region, as had greater alpha than goat Minnesota trials. Beta differed absence STEC, while samples, it events. Actinobacteria negatively decreased samples. Grazing did not significantly affect composition, no interaction observed soil. The results suggest that microbiome dynamics ICLS are animal regional factors, interactions communities having minimal impact.