Talukder Sudipta, Yang Frederick, Klopatek Sarah, Oltjen James, Yang Xiang
Department of Animal Science, University of California-Davis, 2237 Meyer Hall, Davis, CA, 95616, USA.
BMC Microbiol. 2025 Jun 6;25(1):351. doi: 10.1186/s12866-025-04073-6.
Shiga toxin-producing (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, = 21), 20-month grass-fed (20GF, = 18), 25-month grass-fed (25GF, = 16), and 45-day grain-fed after 20-month grass-fed (GR45, = 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 ( < 0.05) fecal STEC population than the grass-fed feeding system. However, the fecal prevalence of STEC was lower ( < 0.05) only in the GR45 compared to the grass-fed groups, while the CON group did not differ ( > 0.05) in STEC prevalence. In terms of STEC population, GR45 was more similar to the grain-fed group. Alpha diversity was greater ( < 0.05) in CON, followed by 25GF, with GR45 being the only system where alpha diversity decreased ( < 0.05) from baseline to harvest. Beta diversity showed a notable difference ( = 0.913, = 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 ( < 0.0001) Firmicutes abundance, followed by 20GF, while the lowest levels were observed in 25GF and CON. Among bacterial families, was more abundant in grass-fed groups, whereas 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.
无论饲养系统如何，产志贺毒素大肠杆菌（STEC）仍然是牛肉生产中一个重大的公共卫生问题。尽管由于气候变化担忧和社交媒体趋势，消费者对草饲牛肉的兴趣有所增加，但不同饲养方式对STEC流行率和数量的安全影响尚未完全了解。因此，本研究的目的是评估谷物饲养和草饲系统对肉牛STEC流行率、数量及其与粪便微生物群相互作用的影响。断奶后的阉牛被分配到四种饲养系统：传统谷物饲养（CON，n = 21）、20个月草饲（20GF，n = 18）、25个月草饲（25GF，n = 16）以及20个月草饲后45天谷物饲养（GR45，n = 13）。在14月龄时采集直肠粪便样本作为基线样本，并在收获前采集样本用于STEC计数、流行率和微生物分析。提取微生物DNA并对16S rRNA基因进行测序以进行微生物群分析。
数据表明，谷物饲养系统中的牛粪便STEC数量高于草饲系统（P < 0.05）。然而，与草饲组相比，仅GR45组的STEC粪便流行率较低（P < 0.05），而CON组的STEC流行率无差异（P > 0.05）。在STEC数量方面，GR45与谷物饲养组更为相似。CON组的α多样性更大（P < 0.05），其次是25GF组，GR45是唯一从基线到收获α多样性降低（P < ）的系统。β多样性显示CON组和GR45组之间粪便微生物组成存在显著差异（P = 0.913，P = 0.001）。厚壁菌门和拟杆菌门是所有饲养系统中的优势菌门。在收获时，GR45组的厚壁菌门丰度最高（P < 0.0001），其次是20GF组，而25GF组和CON组的水平最低。在细菌科中，草饲组中 更为丰富，而谷物饲养的CON组中 更为普遍。与较低STEC流行率相关的微生物群，如拟杆菌门，在STEC阴性样本中更为丰富。
这些发现表明饲养系统会影响STEC水平和肠道微生物多样性，为通过管理微生物群来提高牛肉生产中的食品安全提供了见解。尽管如此，应结合本研究有限的样本量以及与STEC间歇性排出和微生物群组成相关的固有变异性来解释这些结果。
