Antibiotics, in simple terms, are drugs we take to kill pathogenic (disease-causing) bacteria that often attack us. But inside the normal human body, there are several places, where more than 500 different microbial species/flora already reside (We have these by birth). Places like gastrointestinal tract, respiratory tract, urogenital tract, oral cavity etc. The flora aids the body in digestion, metabolism, mineral production, protection etc. These are hence sometimes called as beneficial flora/microflora or simply “good” bacteria. Since antibiotics target microbes especially bacteria, they sometimes end up killing these floras also.
For the intestines, Flora helps in mucosal membrane maintenance, food absorption, immunity etc. Prolonged exposure to antibiotics causes too much destruction of flora from the large intestine, which leaves the person deficient in flora, disturbs body’s digestive mechanism. This is why, often, people who take strong antibiotics suffer from diarrhoea. If the number is reduced below a certain level, this situation can even prove to be lethal. In fact, breastfeading is not recommended for mothers taking antibiotics as this might interfere in the baby's intestinal flora count.
Besides, microbial flora in the gut is already low by nature (gastric juices are acidic and few bacteria can survive). Now think of a person who, because of some infection, has already a low count of these floras and takes antibiotics. A further reduction of this flora population will certainly make the person prone to some other disease or at least severe weakness.