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The origins of our bacteria

Infants have no bacteria at birth but start establishing their skin flora within minutes and digestive tract populations soon after. E. coli, lactobacilli, and intestinal cocci latch on to a baby during birth and become the first colonizers of the infant's digestive tract. Babies get additional bacteria for a reason that scares germophobes: fecal and nonfecal bacteria are everywhere, and people ingest large amounts each day. Fecal bacteria disseminate beyond the bathroom to countertops, desks, refrigerator handles, keyboards, remote controls, and copy machine buttons. Any object repeatedly touched by different people contains fecal bacteria. Newborns get these bacteria every time they handle toys or crawl on the floor, and then put their hands or other objects in their mouth. Adults similarly receive fecal bacteria, called self-inoculation, when touching their hands to the mouth, eyes, or nose. Adults touch their hands to their face hundreds of times a day, and children do it more frequently.

A baby's digestive tract has some oxygen in it so aerobic bacteria and facultative anaerobes prosper there first. E. coli colonizes the gut early on and uses up the oxygen. A population of anaerobes then begins to dominate: Bacteroides, Bifidobacterium, Enterococcus, and Streptococcus make up the common genera. The adult digestive tract distal to the mouth will eventually contain 500 to 1,000 different species of bacteria and a lesser number of protozoa.

Pathogens make up a minority of all bacteria, but the word "germs" brings only bad connotations. A growing number of microbiologists have nonetheless begun to see the potential benefits of exposure to germs. In the 1980s German pediatrician Erika von Mutius investigated the apparent high incidences of asthma and allergies in industrialized nations compared with developing areas. She compared the health of children from households that received little housekeeping with counterparts in well-managed households with regular cleanings. Children who had been exposed to a dirty environment had fewer respiratory problems than children from cleaner surroundings. Von Mutius therefore proposed that a steady exposure to germs might help youngsters develop strong immune systems.

Von Mutius's "hygiene hypothesis" drew criticism from microbiologists and, unsurprisingly, manufacturers of cleaning products. But pediatric allergist Marc McMorris supported the hypothesis, saying, "The natural immune system does not have as much to do as it did 50 years ago because we've increased our efforts to protect our children from dirt and germs."

Questions have not yet been answered on whether continued use of disinfectants and antimicrobial soaps change bacteria at the gene level. Medical microbiologist Stuart Levy has argued that antibiotic overuse combined with overzealous use of antimicrobials leads to bacteria resistant to the chemicals meant to kill them. These bacteria may develop subsequent resistance to antibiotics. Bacteria eject harmful chemicals and also antibiotics from inside the cell by using a pumplike mechanism. If bacteria use the very same pump for chemical disinfectants as for antibiotics, the vision of a new generation of super-resistant bacteria becomes probable. Imagine hospitals where no antibiotics can stop pathogens and few chemical disinfectants can kill them. Doctors and microbiologists have warned that medicine is inching closer to this very scenario.

The body helps native flora defend against pathogens that attach to the skin. The enzyme lysozyme in tears and saliva kills bacteria, and skin oils contain fatty acids that inhibit gram-positive bacteria. If those defenses fail, the immune system sets in motion a hierarchy of defenses meant to find and destroy any foreign matter in the bloodstream.

Dental caries can lead to more serious tooth decay and gum disease, or an infection of the blood if the oral lesions are severe. In plaque, Streptococcus mutans, S. sobrinus, and various lactobacilli (lactic acid-producing bacteria) initiate caries formation by producing acids. Lactic, acetic (also in vinegar), propionic, and formic acid diffuse into the tooth enamel and break it down by demineralization, meaning the removal of minerals such as calcium. Demineralization occurs several times a day in a cycle in which new dietary calcium and phosphate and fluoride from toothpaste replace the lost minerals. Dental caries offer an exception to the rule that native flora do not initiate infection.

On the skin, some bacteria create a nuisance. Skin bacteria consume amino acids, salts, and water excreted by eccrine sweat glands. These glands located all over the body produce copious amounts of watery sweat for cooling. The bacteria also feed on thicker sweat from apocrine glands in the underarms, ear canal, breasts, and external genitalia. These glands tend to activate in times of stress or sexual stimulation. Skin bacteria in these places degrade the sweat's sebaceous oils to a mixture of small fatty acids and nitrogen- and sulfur-containing compounds, all of which vaporize into the air to cause body odor.

Some bacteria such as Staphylococcus live on everyone, but each person also has a unique population of native bacteria that produces a distinctive odor. Scientists have long sought elusive secretions called pheromones that foster communication between people through smell, but I suspect the secretions of native flora will prove to be the human version of quorum sensing. In 2009 anthropologist Stefano Vaglio analyzed the volatile compounds in the sweat of women shortly after childbirth and discovered unique patterns of odor compounds, perhaps to aid mother-infant recognition.

The deodorant and soap industries spend a fortune convincing people to block the natural products made by skin bacteria. Each week hundreds of deodorant-testing volunteers troop into deodorant companies' odor rooms. The volunteers take positions like a police lineup and raise their arms. A team of trained sniffers works its way down the line to "score" the results. Women make up the majority of professional sniffers; the Monell Chemical Sciences Center confirmed in 2009 that women's olfactory systems gather more information from body odors than men's. (Sniffers have sworn that if blindfolded they could identify their mates.) The sniffers assess the best and the worst new deodorants based on underarm odor scores; 0 equals no odor and a score of 10 could clear a room.

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