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The Internet of Things (IoT) is leading today’s digital transformation. Relying on a combination of technologies, protocols, and devices such as wireless sensors and newly developed wearable and implanted sensors, IoT is changing every aspect of daily life, especially recent applications in digital healthcare. IoT incorporates various kinds of hardware, communication protocols, and services. This IoT diversity can be viewed as a double-edged sword that provides comfort to users but can lead also to a large number of security threats and attacks. In this survey paper, a new compacted and optimized architecture for IoT is proposed based on five layers. Likewise, we propose a new classification of security threats and attacks based on new IoT architecture. The IoT architecture involves a physical perception layer, a network and protocol layer, a transport layer, an application layer, and a data and cloud services layer. First, the physical sensing layer incorporates the basic hardware used by IoT. Second, we highlight the various network and protocol technologies employed by IoT, and review the security threats and solutions. Transport protocols are exhibited and the security threats against them are discussed while providing common solutions. Then, the application layer involves application protocols and lightweight encryption algorithms for IoT. Finally, in the data and cloud services layer, the main important security features of IoT cloud platforms are addressed, involving confidentiality, integrity, authorization, authentication, and encryption protocols. The paper is concluded by presenting the open research issues and future directions towards …