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Neomycin can decrease absorption or increase elimination of many nutrients, including calcium, carbohydrates, beta-carotene, fats, folic acid, iron, magnesium, potassium, sodium, and vitamin A, vitamin B12, vitamin D, and vitamin K. Surgery preparation with oral neomycin is unlikely to lead to deficiencies. It makes sense for people taking neomycin for more than a few days to also take a multivitamin-mineral supplement.

Several cases of excessive bleeding have been reported in people who take antibiotics. This side effect may be the result of reduced vitamin K activity and/or reduced vitamin K production by bacteria in the colon. One study showed that people who had taken broad-spectrum antibiotics had lower liver concentrations of vitamin K2 (menaquinone), though vitamin K1 (phylloquinone) levels remained normal. Several antibiotics appear to exert a strong effect on vitamin K activity, while others may not have any effect. Therefore, one should refer to a specific antibiotic for information on whether it interacts with vitamin K. Doctors of natural medicine sometimes recommend vitamin K supplementation to people taking antibiotics. Additional research is needed to determine whether the amount of vitamin K1 found in some multivitamins is sufficient to prevent antibiotic-induced bleeding. Moreover, most multivitamins do not contain vitamin K.

Severe peripheral neuropathy (painful sensations due to nerve damage in the hands and feet) often develops in people taking stavudine or other drugs in its class. People with peripheral neuropathy who were taking one of these drugs were found to be deficient in acetyl-L-carnitine. In a preliminary trial, supplementing with 1,500 mg of acetyl-L-carnitine twice a day resulted in improvement in the neuropathy after six months in people taking stavudine or related drugs. Similar benefits were seen in another study that used the same amount of acetyl-L-carnitine.

A common side effect of antibiotics is diarrhea, which may be caused by the elimination of beneficial bacteria normally found in the colon. Controlled studies have shown that taking probiotic microorganisms—such as Lactobacillus casei, Lactobacillus acidophilus, Bifidobacterium longum, or Saccharomyces boulardii—helps prevent antibiotic-induced diarrhea.

The diarrhea experienced by some people who take antibiotics also might be due to an overgrowth of the bacterium Clostridium difficile, which causes a disease known as pseudomembranous colitis. Controlled studies have shown that supplementation with harmless yeast—such as Saccharomyces boulardii or Saccharomyces cerevisiae (baker’s or brewer’s yeast)—helps prevent recurrence of this infection.

Treatment with antibiotics also commonly leads to an overgrowth of yeast (Candida albicans) in the vagina (candida vaginitis) and the intestines (sometimes referred to as “dysbiosis”). Controlled studies have shown that Lactobacillus acidophilus might prevent candida vaginitis.

Persons with AIDS have developed lactic acidosis and fatty liver while taking AZT and other drugs in its class. AZT can inhibit crucial DNA-related riboflavin activity, which may be normalized by riboflavin supplementation. A 46-year-old woman with AIDS and lactic acidosis received a single dose of 50 mg of riboflavin, after which her laboratory tests returned to normal and her lactic acidosis was completely resolved. More research is needed to confirm the value of riboflavin for preventing and treating this side effect.