Allies and Enemies: How the World Depends on Bacteria (6 page)

The mouth’s supply of nutrients, water, and microhabitats creates

a rich bacterial community. Brushing and flossing remove most but

not all food from between teeth, the periodontal pockets between the

tooth and the gum, and plaque biofilm on the tooth surface, which

holds a mixture of proteins, human cells, and bacterial cells. Anaerobes and aerobes find these places and their relative numbers vary

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allies and enemies

from daytime to night as the level of aeration, flushing with drinks,

and saliva production changes. During the day, more air bathes oral

surfaces and aerobes flourish. At night or during long periods of fast—

ing, the aerobes consume oxygen and anaerobes begin to prosper. By

the nature of their fermentations, anaerobes make malodorous end

products when they digest food. These bad-smelling, sulfur-containing molecules vaporize into the air and become bad breath.

Few bacteria live in the esophagus and stomach with the exception of the spiral-shaped Helicobacter pylori, occurring in half of all people with peptic ulcers. The discovery of H. pylori in the stomach in 1975 dispelled the long-held belief that no microorganisms could withstand the digestive enzymes and hydrochloric acid in gastric juice. Most bacteria traverse the half gallon of stomach fluid at pH 2

by hiding in a protective coat of food particles on the way to the small intestine. H. pylori, however, thrives in the stomach by burrowing into the mucus that coats the stomach and protects the organ from its own acids. Inside the mucus, the bacteria secrete the enzyme urease

that cleaves urea in saliva into carbonate and ammonia. Both compounds create an alkaline shield around H. pylori cells that neutralize the acids.

The pH rises in the intestines and bacterial numbers increase a

millionfold from about 1,000 cells per gram of stomach contents, which to a microbiologist is a small number. Humans, cows, pigs, termites, cockroaches, and almost every other animal rely on intestinal bacteria to participate in the enzymatic digestion of food. The numbers reach 1012 cells per gram of digested material. Monogastric animals such as humans and swine absorb nutrients made available by the body’s enzymes as well as nutrients produced by bacteria. When

the bacteria die and disintegrate in the intestines, the body absorbs

the bacterial sugars, amino acids, and vitamins (B-complex and vitamin K) the same as dietary nutrients are absorbed. Cattle, goats, rabbits, horses, cockroaches, and termites, by contrast, eat a fibrous diet high in cellulose and lignin that their bacteria must break down into compounds called volatile fatty acids. Glucose serves as the main energy compound for humans, but volatile fatty acids power ruminant animals (cattle, sheep and goats, elephants, and giraffes) and animals with an active cecum (horses and rabbits).

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Rumen bacteria carry out anaerobic fermentations. Almost every

organic compound in the rumen becomes saturated there by fermentative bacteria before moving on to the intestines. As a result, ruminants such as beef cattle deposit saturated fats in their body tissue.

Nonruminant animals, such as pigs and chicken, carry out fermentations to a lesser extent and their meat contains less saturated fat.

How important are all these bacteria in keeping animals alive?

Germfree guinea pigs grow smaller than normal, develop poor hair

coat, and show symptoms of vitamin deficiency compared with animals with a normal microbial population. Germfree animals also

catch infections more than populated animals. On the upside,

germfree animals never experience tooth decay!

Bacteroides, Eubacterium, Peptostreptococcus, Bifidobacterium, Fusobacterium
,
Streptococcus , Lactobacillus , and E. coli of the human intestines also produce heat in the same way wine fermentations produce heat. This heat loss is inefficient for the bacteria—any energy that dissipates before it can be used is lost forever—but the

body uses it to maintain body temperature. The large numbers of

normal intestinal bacteria also outcompete small doses of food illness

bacteria such as
Salmonella
,
Clostridium
, Bacillus , Campylobacter , Shigella, Listeria , and E. coli
.

E. coli
is the most notorious of foodborne pathogens and also the most studied organism in biology. In fact, E. coli plays a minor role in the digestive tract; other bacteria outnumber it by almost 1,000 to one.
E. coli has become the number one research tool in microbiology for two reasons. First, this microbe cooperates in the laboratory.

E. coli
is a facultative anaerobe, meaning it grows as well with oxygen as without it. It requires no exotic nutrients or incubation conditions, and it doubles in number so rapidly that a microbiologist can inoculate it into nutrient broth in the morning and have many millions of cells that afternoon. The second reason for using
E. coli
in biology relates to the ease of finding it in nature: The human bowel and that of most other mammals produce a constant supply.

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 , 30

allies and enemies

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 coun—tertops, 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 housekeep—

ing with counterparts in well-managed households with regular clean—

ings. 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.”

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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 gen—

italia. These glands tend to activate in times of stress or sexual stimulation. Skin bacteria in these places degrade the sweat’s sebaceous oils to 32

allies and enemies

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.

One planet

During the Golden Age of Microbiology, bacteria were viewed as unrelated individualists. Pasteur studied the bacteria that made lactic acid by fermenting sugar. Joseph Lister focused on germs causing infections in hospital patients. Robert Koch discovered the anthrax pathogen, Bacillus anthracis , and delved into the processes of bacterial disease. He would develop a set of criteria (Koch’s postulates) that gave birth to today’s methods for diagnosing infectious disease. Not until microbial ecology developed did biologists recognize the interrelated world of bacteria as well as the relationship between environmental bacteria and humans.

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Staphylococcus epidermidis
contributes to body odor, a bacteria-human connection easily detected. But thousands of hidden bacterial activities shape the very ecology of the planet. In soil, Azotobacter pulls nitrogen from the air, chemically rearranges it, and hands it off to Nitrosomonas , which changes the nitrogen again and shuttles it to Nitrobacter.
Nitrobacter then secretes the nitrogen in the form of nitrate, which disseminates throughout soils. Some of the nitrate reaches the roots of legumes such as clover or soybeans. Inside the plant roots anaerobic Rhizobium absorbs the nitrate and converts it to a form the plant can use. This process is vital in replenishing nitrogen that higher organisms need.