Bellotti Gabriele, Cortimiglia Claudia, Antinori Maria Elena, Cocconcelli Pier Sandro, Puglisi Edoardo
Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy.
Microb Genom. 2025 Apr;11(4). doi: 10.1099/mgen.0.001391.
Microbial biostimulants (MBs) offer a sustainable approach to agriculture by helping to reduce reliance on synthetic fertilizers. However, as MBs are intentionally released into the environment, their safety should be rigorously assessed. While taxa with qualified presumption of safety (QPS) benefit from established safety indications, non-QPS taxa lack such guidance. To address this gap, we propose a pipeline combining whole genome sequencing (WGS) and extensive literature search (ELS) data to evaluate microbial safety. We analysed public genomes of three QPS species (, , ) and four non-QPS genera (, , , ), screening them for virulence factors (VFs), antimicrobial resistance (AMR) genes and mobile genetic elements (MGEs). Results confirmed the safety of QPS taxa, revealing no VFs and only a few intrinsic and non-clinically relevant AMRs. Among non-QPS taxa, VF hits were more prevalent in and spp., though they were mostly related to beneficial plant interactions rather than pathogenicity. AMR genes in non-QPS taxa were primarily associated with efflux pumps or were sporadically distributed. Notably, the only genus-wide pattern observed was that most and genomes harboured chromosomally encoded -lactamases sharing similar genetic structures; however, the detected -lactamase () genes were distantly related to clinically relevant variants, and the absence of MGEs suggests a low risk of horizontal gene transfer, indicating the overall safety of these genera. In general, this WGS-ELS framework provides a robust tool for assessing the safety of non-QPS MBs, supporting regulatory decision-making and ensuring their safe use in sustainable agriculture while safeguarding public health.
微生物生物刺激素（MBs）通过帮助减少对合成肥料的依赖，为农业提供了一种可持续的方法。然而，由于MBs是有意释放到环境中的，其安全性应受到严格评估。虽然具有合格安全推定（QPS）的分类群受益于既定的安全指示，但非QPS分类群缺乏此类指导。为了弥补这一差距，我们提出了一种将全基因组测序（WGS）和广泛文献搜索（ELS）数据相结合的流程，以评估微生物的安全性。我们分析了三种QPS物种（ 、 、 ）和四个非QPS属（ 、 、 、 ）的公共基因组，筛选其中的毒力因子（VFs）、抗菌抗性（AMR）基因和移动遗传元件（MGEs）。结果证实了QPS分类群的安全性，未发现毒力因子，仅发现了一些内在的且与临床无关的抗菌抗性。在非QPS分类群中，毒力因子命中在 属和 属物种中更为普遍，不过它们大多与有益的植物相互作用而非致病性有关。非QPS分类群中的抗菌抗性基因主要与外排泵相关或呈零星分布。值得注意的是，观察到的唯一全属模式是，大多数 属和 属基因组含有染色体编码的具有相似遗传结构的β-内酰胺酶；然而，检测到的β-内酰胺酶（ ）基因与临床相关变体的亲缘关系较远，且缺乏移动遗传元件表明水平基因转移的风险较低，这表明这些属总体上是安全的。总体而言，这种WGS-ELS框架为评估非QPS MBs的安全性提供了一个强大的工具，支持监管决策，并确保它们在可持续农业中的安全使用，同时保障公众健康。
