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Consumption of antibiotics can have a harmful effect on the good bacteria in the body

Antibiotics are one of the most important inventions in the field of medicine, with their ability to kill bacteria that pose a danger to humans. However, over a period of time, it was also discovered that the use of antibiotics has several constraints; they pose a danger to the beneficial bacteria present in the human body (including the bacteria in the human gut that play a key role in digestion), and the growing resistance by bacteria to these antibiotics. The increased use of antibiotics for even non-essential needs leads to a few bacteria developing resistance to these antibiotics, and over a period of time, you get a new class of bacteria that are resistant to these drugs, and you need more effective antibiotics (and has also lead to the development of a new class of superbugs that are posing grave dangers to the medical industry).
Now, research indicates that when people are given even a mild dose of antibiotics, these antibiotics have a harmful effect on the bacteria present in the human gut and these bacteria need a lot of time to recover. The other problem being that when these good bacteria are affected, there is a space that is then occupied by more harmful bacteria. Further, the interaction between good bacteria and health is not fully understood (link to article):

Even seemingly gentle antibiotics may severely disrupt the balance of microbes living in the gut, with unforeseen health consequences, U.S. researchers reported. An intimate study of three women given ciprofloxacin showed the drug suppressed entire populations of beneficial bacteria, and at least one woman took months to recover. The study, published in the Proceedings of the National Academy of Sciences, supports the common wisdom that antibiotics can damage the ‘good’ germs living in the body.
“By one week after the end of each course, communities began to return to their initial state, but the return was often incomplete.” More and more studies support the idea that humans and other animals have a symbiotic relationship with germs. Microbes in the intestines help digest food and ‘good’ germs can take up space and keep bad germs away.

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