The Hygiene Hypothesis

Numerous studies suggest links between certain disorders and a lack of exposure to particular microbes. Children raised on farms, for example, develop fewer autoimmune disorders than urban children [source: Zimmer].

Along similar lines, people with asthma possess a different set of microbes than nonasthmatics. Reduced microbe exposure rates in the developed world could explain the recent uptick in occurrences of asthma and atopy -- a genetic predisposition toward developing allergic reactions [sources: Olszak et al.; Reibman et al.; Zimmer].

Bacteria: Flush With Success

Bacteria are arguably the most successful life-forms on Earth. You can find them clustered around deep-sea vents, buried far underground or teeming throughout larger organisms, including us. Our mouths alone contain hundreds to thousands of species, divided into colonial neighborhoods across our teeth, gums and tongue. Our lungs, once thought microbe-free, house 2,000 per square centimeter, and our guts could host as many as 25,000-30,000 different species [sources: Grady; Zimmer].

While we might think of them as microscopic menaces -- the sources of such delights as bacterial meningitis, urinary tract infections and food poisoning -- without bacteria, life as we know it would not exist. Starting 2.7-2.8 billion years ago, cyanobacteria released the first oxygen into the atmosphere; today, bacteria convert atmospheric nitrogen into something plants can use and recycle nutrients from dead organisms into the ecosystem [sources: Biello; Ingham; Farquhar, Bao and Thiemens].

Bacteria and other microbiota perform similar functions in our bodies. Gut microbes produce vitamins and reduce tough plant compounds into digestible slurry [source: Zimmer]. Within the immune system, bacteria help maintain skin's protective qualities, and nasal microbes produce an antibiotic shield against airborne germs. Moreover, microbes keep the immune system in check by limiting harmful swelling. It isn't a stretch to see how they might therefore play a role in inflammation-associated disorders, such as obesity, cardiovascular disease, type 2 diabetes and inflammatory bowel disease (IBD) [sources: Gewirtz; Zimmer; Zimmer].

Microbes also make healthier babies. Breast milk packs 600 species of bacteria and provides sugars that feed a baby's developing gut bacteria [sources: Hunt et al.; Zimmer; Zivkovic et al.]. According to a June 2011 PLoS One study, a woman's vaginal microbiome changes drastically when she becomes pregnant. Among other effects, this new environment might prepare newborns to digest breast milk [sources: Aagaard et al.; Zimmer]. Some studies suggest children born via cesarean section might be more prone to skin infections from methicillin-resistant Staphylococcus aureus (MRSA), a staph germ that resists first-line antibiotics such as penicillin and amoxicillin. Such children could also face greater risk of developing allergies or asthma [sources: CDC; Zimmer].

Exposure to certain microorganisms trains a child's developing immune system [source: Zimmer]. It also probably provides a natural defense against inflammatory bowel disease (IBD), a chronic or recurring inflammation of the gastrointestinal tract caused by a haywire immune response [sources: Olszak et al.; Zimmer]. IBD, which includes ulcerative colitis and Crohn's disease, ranks among the five most widespread gastrointestinal diseases in the United States and racks up health care costs of $1.7 billion annually [source: CDC].

When the stakes are so high, particularly for patients with life-threatening intestinal maladies, doctors have started thinking outside the box -- and inside the colon.