Lactobacillus acidophilus occurs naturally in the digestive tract and vagina, helping to create an acidic and healthy environment. When there is too little of this "good" bacteria present, bad bacteria like E. coli can overgrow, leading to infection. Acidophilus supplements are used to combat these situations; however, they are not without their side effects.
Diarrhea
Acidophilus causes a dramatic change in the digestive tract. If your body isn't used to it, an upset stomach is likely, including diarrhea. You may notice painful cramps and gas along with loose, watery stools.
Bloating
As your body adjusts to a proliferation of good bacteria in the gut, bloating can be expected. This may be painful or just uncomfortable. However, most of the time bloating passes within a few days or so.
Nausea
Some experience an upset stomach or nausea when taking acidophilus supplements or eating yogurt that contains these active cultures. That being said, if you vomit or feel very ill, it may be best to discontinue use of the supplement and seek medical advice.
Vaginal Itching
Acidophilus is sometimes used to maintain a healthy pH balance in the vagina. It is when this balance is thrown off and too many bad bacteria proliferate that yeast infections occur. However, placing acidophilus in the vagina can cause temporary itching and burning until your body adjusts.
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Severe Side Effects
Most of the time, reactions to acidophilus are mild. However, in some cases, the side effects may be more severe and include dizziness, hives, swelling of the lips, mouth or throat and breathing problems. That being said, using acidophilus when your immune system is very weak can do more harm than good, causing an overgrowth of bacteria and a potentially bad infection.