16Silver (Ag) has been gaining broad attention due to their antimicrobial activities and the 17 increasing resistance of bacteria to commonly prescribed antibiotics. However, various aspects 18 of the antimicrobial mechanism of Ag have not been understood, including how silver affects the 19 motility of bacteria, a factor that is intimately related to bacterial virulence. Here we report our 20 study on the antibiotic effects of Ag + ions on the motility of E. coli bacteria using swimming and 21 tethering assays. We observed that the bacteria slowed down dramatically when subjected to 22Ag + ions, providing direct evidence showing that Ag inhibits the motility of bacteria. In addition, 23 through tethering assays, we monitored the rotation of flagellar motors and observed that the 24 tumbling frequency of bacteria increased significantly in the presence of Ag + ions. Furthermore, 25the rotation of bacteria in the tethering assays were analyzed using hidden Markov model 26 (HMM); and we found that Ag + -treatment led to a significant decrease in the tumbling-to-running 27 transition rate of the bacteria, suggesting that the rotation of bacterial flagellar motors was 28 stalled by Ag + ions. This work provided a new quantitative understanding on the mechanism of 29 Ag-based antimicrobial agents in bacterial motility. 30 31 32Keywords: hidden Markov model, antibiotics, E. coli, motility, tethering assay. 33 34 42 towards understanding the antimicrobial mechanism of Ag, suggesting that Ag caused 43 multidirectional damages to bacteria, including DNA damage, membrane disruption, free radical 44 generation (ROS), and loss of ATP production [7,9, 10, 11, 12, 13]. However, various aspects of 45 the antimicrobial mechanism of Ag remain elusive, especially that the temporal resolution for 46understanding the Ag-caused damages in bacteria Ag is still limited [7, 14,15]. This includes how 47 silver affects the motility of bacteria, which is tightly coupled to bacterial virulence [16]. 48 49Motility is essential to many bacteria for detecting and pursuing nutrients, as well as avoiding 50and fleeing from toxicants. Certain bacteria, such as Escherichia coli (E. coli), use flagella to move 51 in aqueous environments [17]. E. coli flagella are filaments extending outward from the 52 bacteria [18]. The flagella are connected to and driven by motors embedded in the bacterial 53 membrane through hooks [19]. For E. coli -peritrichous bacteria with flagella covering their entire 54 surfaces, their movement depends on the rotation direction of their flagella [17, 19]. When 55 flagella rotate counterclockwise (CCW), they are bundled and propel the bacteria to move 56 directionally (i.e., running) for purposeful movement toward chemical attractants or away from 57repellents [17, 20]; when flagella rotate clockwise (CW), they are splayed out, resulting in 58 reorientation (i.e., tumbling) of the bacteria [17, 20]. The E. coli flagella contains mainly three 59 parts: the filament, the hook, and the basal body [17, 20]. The basal body cons...