The intestinal commensal microbial community (or microbiota) is composed of several microorganisms that, among other functions, are beneficial for the protection against infectious agents. When the microbiota is altered many bacteria are lost, compromising the protective ability and enabling invasion by harmful bacteria. Antibiotics, despite being the best way to treat infections, can lead to changes in the microbiota and to the loss of some of these protective bacteria.
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Source: Phys.org