Abstract：
The discharge from pig farms presents significant challenges to the environment and human health, specifically regarding the dissemination of antimicrobial resistance (AMR). Fermentation bed culture has emerged as an increasingly popular and environmentally friendly pig farming model in China, as it minimizes the release of harmful substances into the environment. However, there remains a limited understanding of the occurrence and dynamics of microbiome and antibiotic resistome in fermentation bed culture. Herein, we collected fermentation bed materials (FBM) from four fermentation bed culture pig farms with varying service ages and investigated their bacterial communities, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metal resistance genes (MRGs) and potential antibiotic-resistant bacterial hosts through metagenomics. Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota were identified as the dominant phyla present in the FBM. In total, we detected 258 unique ARGs in the FBM samples, with 79 core ARGs shared by all FBM samples, accounting for 95 % of the total ARG abundance. Our results revealed significant variations in microbial communities and ARG profiles across varying service ages of FBM. Compared to long-term FBW, short-term FBM exhibited higher numbers and abundances of ARGs, MRGs and MGEs, along with higher levels of potential bacterial pathogens and high-risk ARGs. Further analysis of metagenome-assembled genome (MAG) indicated that the putative hosts of ARGs primarily belonged to Pseudomonadota, Actinomycetota and Bacillota. Alarmingly, among the 80 recovered ARG-carrying MAGs, 23 MAGs encoded multi-resistance, including clinically significant species that require urgent attention. Overall, this study provided valuable insights into the temporal patterns of antibiotic resistome and bacterial communities within FBM, enhancing our understanding of FBM in pig farming. The findings could potentially contribute to the development of effective strategies for evaluating and regulating fermentation bed culture practices in pig farming.
摘要：
养猪场的排放对环境和人类健康提出了重大挑战，特别是关于抗菌素耐药性(AMR)的传播。发酵床养殖已成为我国日益流行的一种环保养猪模式,因为它最大限度地减少了有害物质向环境中的释放。然而,对发酵床培养中微生物组和抗生素抗性组的发生和动态的理解仍然有限。在这里，我们收集了四个不同服务年龄的发酵床培养猪场的发酵床材料（FBM），并调查了它们的细菌群落，抗生素抗性基因（ARGs），移动遗传元件(MGEs)，金属抗性基因（MRGs）和潜在的抗生素抗性细菌宿主通过宏基因组学。Pseudomonadota,放线菌,拟杆菌和杆菌被鉴定为存在于FBM中的优势门。总的来说,我们在FBM样本中检测到258个独特的ARG，所有FBM样本共享79个核心ARG，占总ARG丰度的95%。我们的结果表明，在FBM的不同服务年龄中，微生物群落和ARG谱存在显着差异。与长期FBW相比，短期FBM表现出更高的ARGs数量和丰度，MRG和MGE，以及更高水平的潜在细菌病原体和高风险ARGs。对宏基因组组装基因组（MAG）的进一步分析表明，ARGs的推定宿主主要属于Pseudomonadota，放线菌和芽孢杆菌。令人震惊的是,在80个回收的携带ARG的MAG中，23个MAG编码的多电阻，包括临床上需要紧急关注的重要物种。总的来说,这项研究为FBM内抗生素耐药性和细菌群落的时间模式提供了有价值的见解，加强我们对养猪业FBM的理解。这些发现可能有助于制定有效的策略来评估和调节养猪业的发酵床培养方法。
