Antibiotics are often necessary for the treatment of serious infections, such as pneumonia bacteraemia or meningitis. They can also be used to manage infection in people with cystic fibrosis or compromised immune systems. There is also prophylactic use to avoid infection, such as following an operation or lab exposure to a pathogen. What alternatives could be used in these circumstances?
The full article on the study you referred to earlier on a link between Candida and an increase in allergies can be found
here. I'm not sure how applicable it would be to humans. The mice would have been raised in sterile conditions, so their immune system would be more naive, and there would be less diversity in their microflora, making it easier to be knocked out by the antibiotic.
Yeast, including the opportunistic pathogen Candida albicans, can be found as part of the commensal microflora of most mucosal surfaces of the body, including the gut and upper respiratory tract. Of course long term use of antibiotics (particularly broad-spectrum) will favour yeast growth as they remove competition.
The immune response to Candida albicans is production of interleukin (IL)-10 but not of IL-12 or interferron (IFN) gamma
(link). IL-12 and IFN gamma are important in the Th1 immune response which is responsible for killing intracellular pathogens. It is thought that allergies develop when the immune system is skewed towards a Th2 response
(a bit more on Th1 and Th2 responses).
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