The normal flora synthesize and excrete vitamins which can be absorbed as nutrients by their host. For example, in humans, enteric bacteria secrete Vitamin K and Vitamin B12, and lactic acid bacteria produce certain B-vitamins.

The normal flora prevent colonization by pathogens by competing for attachment sites or for essential nutrients. This is thought to be their most important beneficial effect, which has been demonstrated in the oral cavity, the intestine, the skin, and the vaginal epithelium. In some experiments, germ-free animals can be infected by 10 Salmonella bacteria, while the infectious dose for conventional animals is near 106 cells.

The normal flora may antagonize other bacteria through the production of substances which inhibit or kill nonindigenous species. The intestinal bacteria produce a variety of substances ranging from relatively nonspecific fatty acids and peroxides to highly specific bacteriocins, which inhibit or kill other bacteria.

The normal flora stimulate the production of natural antibodies. Since the normal flora behave as antigens in an animal, they induce an immunological response, in particular, an antibody-mediated immune (AMI) response. Low levels of antibodies produced against components of the normal flora are known to cross react with certain related pathogens, and thereby prevent infection or invasion. Antibodies produced against antigenic components of the normal flora are sometimes referred to as “natural” antibodies, and such antibodies are lacking in germ-free animals.

Beneficial bacteria reinforce the mucosal barrier of the intestines, which is associated with the gut associated lymph tissue (GALT) helping to prevent pathogens, toxins and allergens from gaining access to the rest of the body. In this way, their presence “teaches” the immune system which allergens and toxins are tolerable and which need to be disposed of.

Some bacteria have a stimulating effect on the immune system, by increasing T–cell counts, for example. In a recent study reported by the Annals of Nutrition and Metabolism, the number of certain T–lymphocytes that target cytotoxins (T2, T3 and T4) jumped by more than 28% in healthy young female test subjects after they ate conventional yogurt daily for one month.

Other good bacteria produce natural antibiotics and antifungals; for instance, Streptococcus salivarius manufactures an antiseptic that neutralizes the sulfur compounds responsible for bad breath (halitosis). Friendly flora also keep unfriendly bacteria in check by depriving them of nutrients and secreting acids (acetic, lactic, and formic) that create a hostile environment for pathogens.

Beneficial flora metabolize and recycle hormones, including estrogen, thyroid hormones, and phytoestrogens from food sources, which can help offset symptoms of menopause and PMS. In this way, they help maintain proper hormonal balance, and may protect bone and breast health as well.

They also detoxify drugs and other potentially harmful compounds we put into our systems on purpose or by accident. There is evidence that some probiotics may have anti-tumor, anticancer effects by helping us metabolize specific food components (like antioxidants and flavonoids) into useable forms.

Stress increases the production of HCL in the stomach, neurotensin in the gut, mucous production from mast cells and basophils, alterations in the mucosa leading to leaky gut, and an exaggerated IgG and IgE response.

This increases IBS symptoms, decreases nutrient absorption, lowers immunity and increase further cortisol and CRH deposition.