Modern medicine has conjured a deep fear of microbes that has led to gross over-use of antibiotics, most commonly for sinus and ear infections. Antibiotic literally means "against life", but is largely used to refer to medications that kill bacteria. Many of these medications are derived from mycotoxins produced by fungi for the purpose of killing competing bacteria. What most doctor's don't tell you is that many of the antibiotics they prescribe kill not only harmful bacteria, but also health promoting bacteria. Not only that, but when bacteria are suppressed, fungi can go into a feeding frenzy and multiply like crazy. And most fungi are not beneficial. What's worse, antibiotics also depress our immune system, allowing unaffected microbes to flourish. And furthermore, over-use of antibiotics creates antibiotic-resistant strains of bacteria that can take advantage of any depressed immune system. Consequently, antibiotics should be reserved for only the most severe bacterial infections.
Most people don't realize there are many more microbes in our bodies than human cells, by at least a factor of two or three. We are really symbiotic cultures of human cells and microbes. Most of these microbes are in our digestive system and can weigh as much as three or four pounds. When we are healthy, most of the microbes are beneficial bacteria that help us digest our food and even add nutrients to our system and help support our immune health. This is "symbiosis". Taking powerful antibiotics greatly damages this symbiotic system by killing the beneficial bacteria and allowing harmful microbes, mainly fungi and resistant bacteria, to multiply, causing "dysbiosis". These unfriendly microbes can damage the mucosal lining of the intestines allowing undigested harmful proteins and chemicals to enter the body and the bad microbes can also generate toxins that are absorbed into our body. Dysbiosis often leads to food allergies and may trigger auto-immune diseases, which are malfunctions of our immune system. Dysbiosis may also cause or contribute to irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD).
We are born without beneficial microbes in our digestive system, but mother's milk provides a host of beneficial microbes that quickly colonize our infant digestive systems. The microbes change in composition over time, influenced largely by the foods we eat. These beneficial microbes serve as our first line of defense in combating harmful microbes. When they are healthy, they can out-compete undesirable microbes and may even kill them directly. So, it is imperative to eat foods that promote the beneficial microbes. These can be foods that feed the microbes or foods that actually have live beneficial microbes to re-enforce the supply in our system. Foods with live beneficial microbes are called probiotic, which literally means "for life". Some of the best probiotic foods are raw dairy, fermented dairy such as kefir and yogurt, fermented beverages such as kombucha and beet kvass, and lacto-fermented vegetables such as traditional sauerkraut and pickles (unpasteurized). Foods that benefit the good microbes are called "prebiotic" and include vegetable foods with oligosaccharides. Foods high in refined sugar and refined carbohydrates may in quantity promote microbes that are not beneficial. Maintaining proper digestion is critical to our health.
So what can we do to avoid antibiotics? Ideally keep our immune system as healthy as possible to avoid infections in the first place. That means eating plenty of nutrient dense foods and minimizing dietary sugar, refined carbohydrates, and omega-6 fats that can hamper immune function. Also, eating foods with good saturated fats, such as pastured animal and dairy fats and coconut oil, helps to boost immune function. And consuming probiotic foods helps to maintain beneficial bacteria in the digestive system, which in turn helps to boost immune function. Choosing fresh organic foods and staying away from factory processed/packaged foods loaded with harmful food additives, preservatives, and pesticides also helps to reduce the burden on our immune system.
When infections do manage to bring illness, we need to boost the functioning of our immune system - preferably by diet as much as possible. Taking additional probiotic foods and/or supplements may help against many infections, especially gastro-intestinal infections. Herbal medicines may also provide help against many infections. Consult a naturopathic physician or herbal medicine practitioner for diagnosis and prescription. Bone broth is a traditional remedy that can also help our immune system fight many infections, Broth is Beautiful.
For an in depth and well-referenced discussion of dysbiosis read:
"The causes of intestinal dysbiosis: a review"