The risk level (threat to host system homeostasis) and the magnitude and nature of the immune response that needs to be activated are assessed using direct sensing of microorganisms and additional contextual signals (9). The pathogen must overcome several checkpoints (depicted in columns labeled Checkpoint 1–5) before it poses the highest level of threat, resulting in a vigorous immune response (7). Checkpoint 1: Soluble MAMPs initiate cytokine and chemokine production remotely, while MAMPs on whole microorganisms trigger direct microbicidal responses. Checkpoint 2: Vita-PAMPs, such as bacterial mRNA, indicate live microorganisms capable of growth, multiplication, and invasion and trigger enhanced immune responses by activating PRRs. Checkpoint 3: The need and type of immune response to microbial presence varies according to the tissue’s physiology and microenvironment, ensuring appropriate responses. Systemic threats trigger immediate, strong reactions to prevent severe consequences, while local tissue responses are tightly regulated. At the subcellular level, the strongest immune responses are initiated against agents that invade the cytosol. Checkpoint 4: The degree of invasiveness is critical information for the immune system to distinguish between pathogenic and nonpathogenic microorganisms. While commensal bacteria coexist with the host without causing disease, they can become pathogenic if they breach sterile tissues. Invasive forms of microbes expose specific molecules or morphologies that signal potential threats, leading to more robust immune activation. Commensals can act as facultative pathogens under specific conditions. Commensal bacteria can become invasive due to host factors like immunodeficiency, pregnancy, or treatments altering the microenvironment. The immune system and intact physical barriers are crucial for preventing this switch. Invasiveness can be controlled by inhibiting the quorum-sensing system of microorganisms. Checkpoint 5: Virulence. Microorganisms are classified as pathogens or nonpathogens based on their ability to cause disease, correlating with virulence factors that disrupt host barriers and invade tissues.