• Friendly bacteria are essential to the proper development of the immune system.
  • All individuals have a different composition of bacterial species in their guts starting at birth.
  • The Western world’s diet and emphasis on a bacteria-free environment may have contributed to a rise in certain diseases, such as chronic inflammatory diseases, and allergies.


Friendly bacteria are essential to the proper development of the immune system; additionally, they protect us against microorganisms that may cause disease, and aid in the digestion and absorption of food and nutrients. 1 How the individual interacts with the microorganisms in his or her body – and how the microorganisms themselves interact – has an effect on health and well-being. This intricate balancing act can be disrupted: 2

  1. through the use of antibiotics, which kill friendly bacteria along with ‘bad’ bacteria, and may disrupt the homeostasis of the intestinal flora; or
  2. by disease-causing microorganisms, including bacteria, yeasts, fungi, parasites and viruses.

Predating human existence, bacteria are some of the oldest living organisms on earth and indeed exist in greater numbers than do humans. Bacteria have a negative connotation, frequently linked to disease, dirt, decay, and mortality; however, human survival is quite dependent on a truce with the bacterial world. A bacterial colony is a tremendous force; in less than 10 minutes, a colony can double in size.


While infants are born with a gut that is virtually sterile, it is quickly colonized by both maternal flora and environmental flora. The guts of babies born vaginally are colonized by fecal and vaginal bacteria from their mothers, predominantly by Bifidobacteria, microbes that are supported by breast milk ingestion. Conversely, those infants born by Caesarean section are exposed to a mixture of potentially harmful bacteria like Staphylococcus and Acinetobacter from healthcare workers and/or from the hospital environment.3


Without good bacteria in our gastrointestinal tract, our immune systems would not function properly, and would certainly be more susceptible to disease. Beneficial bacteria help protect against microorganisms that cause disease, and aid in the digestion and absorption of food and nutrients. But the gut is also home to ‘bad’ or harmful bacteria that can colonize the gut, invade the body, or release disease-causing toxins. Autoimmune disorders, depression, allergies and several other illnesses may be associated with an unhealthy balance of bacterial microbiota. Good bacteria, in the form of probiotics, may improve that balance, although it is important to know which species and strain are represented.

Antibiotics have been proven useful in combating bad bacteria, but because they can also eradicate good bacteria, they should be used with caution.


Our Western world promotes a sanitized, bacteria-free and sterile environment. This widespread adaptation of modern hygiene practices means that the changes to the human body’s personal ‘ecosystem’ have been too rapid for our bodies to adjust – and thus we have seen a rise in autoimmune diseases and immunological disorders. Peanut allergies, Crohn’s disease, asthma, etc., have also increased significantly. It is to our advantage that we be regularly exposed to a variety of bacteria, moulds and fungi, since insufficient exposure to infectious diseases and environmental microorganisms can result in immune dysfunction according to the hygiene hypothesis.

“There has been much speculation as to why certain diseases and conditions that involve the immune system acting against the body (eg. asthma, Crohn’s disease, allergies) are increasing in developed countries. The hygiene hypothesis is the thought that modern hygiene practices (sanitization, bacteria reduction, sterile environments) have led to changes in human body’s personal “ecosystem”. With the increasing understanding that this ecosystem interacts with the immune system of its host, inadequate interactions have led to “immune dysfunction”. This “immune dysfunction” has in turn led to the host immune system causing certain diseases, disorders and allergies according to this theory.”

Dr. David R. Mack, MD, FRCPC, Professor, Department of Pediatrics, Faculty of Medicine,
University of Ottawa and Chief, Division of Gastroenterology, Hepatology & Nutrition,
Department of Pediatrics, Children’s Hospital of Eastern Ontario (CHEO)