The objective of probiotic therapy is to optimize the body’s defense mechanisms with microbiotics and autovaccines and, possibly, to replace antibiotics with probiotics.

Probiotics are increasingly becoming established as a therapeutic option in addition to antibiotics. Antibiotics and probiotics are not necessarily antagonistic. Antibiotics are still the last resort in cases of severe bacterial or parasitic infections. Positive effects of antibiotics can be maximized and negative effects on the immune system minimized by strictly controlling their application.

Probiotics are useful therapeutic tools in numerous cases of acute and, above all, chronic infections. Prerequisite for applying probiotics is the critical delimitation of life-threatening infections or imminent complications. Probiotics can reduce the negative effects of antibiotics, e. g., problems posed by resistance, and optimize their positive effects on immunological functions.

Homo sapiens represents only a snapshot in evolution and will continue to evolve in the future. From the very beginning, microbes played an important role. Mutual dependencies and requirements developed, and these are reflected in complex functional areas and diverse differentiations of structural interrelationships. The term symbiosis is often used in this connection. However, the definition of symbiosis includes a range of partnerships, such as parasitism, neutralism, commensalism, and mutualism. In a partnership such as parasitism, only one of the partners is the beneficiary, namely the parasite, whereas the other partner is harmed by the parasite. A symbiotic association in which partners coexist without mutual interaction and without obvious advantages or disadvantages is called neutralism. Commensalism is a close association from which only one of the two partners benefits without causing harm to the other partner. A partnership in which both partners benefit from each other is called mutualism (mutualistic symbiosis – coexistence for mutual benefit).

Much of our knowledge on the interaction between unicellular and multicellular organisms comes from gnotobiology, the science dedicated to studying animals raised in a germ-free environment, comparing them with microflora-associated normal animals, and also studying monoflora-associated or polyflora-associated animals.

The structures of the mucosa as interface and the colonization of this surface by symbiotic microorganisms represent a phylogenetically and ontogenetically determined functional unit and are part of the innate immune system. In stable layers of microbial populations, such as the intestinal flora, mutualistic and commensal microorganisms are in the majority. Together with the immune system, this majority keeps the minority of opportunists under surveillance and usually restricts the number of germs.

– resistance to colonization: the control over colonization with endogenous, facultative pathogenic germs and heterogenous invaders

– stimulation and stabilization of epithelial integrity

– stimulation and differentiation of lymphatic organs.

Any external or internal disturbance of the well-balanced equilibrium of the unicellular microbes with the multicellular body of Homo sapiens has more or less severe consequences for physiological functions and health.

A typical sign of the pathogenicity of microorganisms is their ability to break through the barriers of the innate defense system and to propagate in the internal milieu. In the classic case, these are natural pathogens or obligatory pathogens that are normally not members of the partnership between man and microbes, i. e., they are nonsymbionts. The adaptive immune system is responsible for dealing with the assault by such pathogens.

A microorganism can develop pathogenic properties only when it possesses genes that code for pathogenicity factors and when certain conditions lead to the expression of these genes. In the genomes of many pathogenic species of bacteria, transfer and recombination processes have established certain genetic structures that are called pathogenicity islands. These are DNA fragments that occur as genomic islands also in many non-pathogenic microbes. Their genetic codes include information for metabolic functions, secretion processes, or resistances. In terms of evolutionary biology, such genetic islands may be advantageous for microorganisms under certain conditions of selection.

Microorganisms in the environmental reservoir, as well as in symbiotic microbial populations, are constantly involved in the exchange of genes. Pieces of genetic information are continually mixed through horizontal gene transfer, and new microbial variants are thus formed.