Effect of conventional grain-fed and grass-fed feeding systems on fecal microbiota and shiga toxin-producing Escherichia coli in beef cattle

Shiga toxin-producing Escherichia coli (STEC) remains a significant public health concern in beef production, regardless of feeding systems. While consumer interest in grass-fed beef has increased due to climate change concerns and social media trends, the safety implications of different feeding practices on STEC prevalence and populations are not fully understood. Therefore, the objectives of this study were to evaluate the effects of grain-fed and grass-fed feeding systems on STEC prevalence, population, and its interaction with the fecal microbiota in beef cattle. Post-weaning steers were assigned to four feeding systems: Conventional grain-fed (CON, n = 21), 20-month grass-fed (20GF, n = 18), 25-month grass-fed (25GF, n = 16), and 45-day grain-fed after 20-month grass-fed (GR45, n = 13). Rectal fecal samples were collected at 14 months of age as baseline and pre-harvest for STEC enumeration, prevalence, and microbial analysis. The microbial DNA was extracted and sequenced for 16 S rRNA gene for microbiota analysis. Data demonstrated that cattle in grain-fed feeding system had a higher (P < 0.05) fecal STEC population than the grass-fed feeding system. However, the fecal prevalence of STEC was lower (P < 0.05) only in the GR45 compared to the grass-fed groups, while the CON group did not differ (P > 0.05) in STEC prevalence. In terms of STEC population, GR45 was more similar to the grain-fed group. Alpha diversity was greater (P < 0.05) in CON, followed by 25GF, with GR45 being the only system where alpha diversity decreased (P < 0.05) from baseline to harvest. Beta diversity showed a notable difference (R = 0.913, P = 0.001) in fecal microbial composition between CON and GR45. Firmicutes and Bacteroidetes were the dominant phyla across all feeding systems. At harvest, GR45 had the highest (P < 0.0001) Firmicutes abundance, followed by 20GF, while the lowest levels were observed in 25GF and CON. Among bacterial families, Peptostreptococcaceae was more abundant in grass-fed groups, whereas Ruminococcaceae was more prevalent in the grain-fed CON group. Microbiota associated with lower STEC prevalence, such as Bacteroidetes, were more abundant in STEC-negative samples. These findings suggest that feeding systems influence both STEC levels and gut microbial diversity, offering insights into managing microbiota to enhance food safety in beef production. Nonetheless, the results should be interpreted in the context of the study’s limited sample size and the inherent variability associated with intermittent STEC shedding and microbiota composition.