In recent years, probiotics have attracted public attention and transformed the social perception of microorganisms, convening a beneficial role/state on human health. With aging, the immune system, body physiology, and intestinal microbiota tend to change unfavorably, resulting in many chronic conditions. The immune-mediated disorders can be linked to intestinal dysbiosis, consequently leading to immune dysfunctions and a cluster of conditions such as asthma, autoimmune diseases, eczema, and various allergies. Probiotic bacteria such as Lactobacillus and Bifidobacterium species are considered probiotic species that have a great immunomodulatory and anti-allergic effect. Moreover, recent scientific and clinical data illustrate that probiotics can regulate the immune system, exert anti-viral and anti-tumoral activity, and shields the host against oxidative stress. Additionally, microbiota programming by probiotic bacteria can reduce and prevent the symptoms of respiratory infections and ameliorate the neurological status in humans. This review describes the most recent clinical findings, including safe probiotic therapies aiming to medicate respiratory infections, allergies, cancer, and neurological disorders due to their physiological interconnection. Subsequently, we will describe the major biological mechanism by which probiotic bacteriotherapy expresses its anti-viral, anti-allergic, anticancer, and neuro-stimulatory effects.