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The bacteria of the human body

Ten trillion cells make up the human body, but more than ten times that many bacteria inhabit the skin, respiratory tract, mouth, and intestines. Microbiologists are fond of pointing out that if all of a person's DNA were mixed with the body's entire bacterial DNA, that person would be genetically more bacterial than human.

About 1,000 different species belonging to 200 genera live on the body rather than in it. An animal's body is a tube. The skin comprises the tube's outer surface, and the gastrointestinal tract from mouth to anus makes up the inner surface. The body's interior of blood, lymph, and organs normally contain no bacteria; these places are sterile. Urine and sweat exit the body as sterile fluids. In plants by contrast, bacteria live on but also inside the plant body.

The skin holds habitats that vary in moisture, oils, salts, and aeration. The scalp, face, chest and back, limbs, underarms, genitals, and feet make up the skin's main habitats, and each of these contains smaller, distinct living spaces. The entire skin surface has about one million bacteria on each square centimeter (cm2) distributed unevenly among the habitats; the dry forearms contain about 1,000 bacteria per cm2, and the underarms have many millions per cm2.

Microbiologists sample skin bacteria by pressing a cylinder about the size of a shot glass open at both ends against the skin to form a cup, and then pouring in a small volume of water. By agitating the liquid and gently scraping the skin with a sterile plastic stick the microbiologist dislodges many of the bacteria. But no method or the strongest antiseptics remove all bacteria from the skin: The skin is not sterile. Staphylococcus, Propionibacterium, Bacillus, Streptococcus, Corynebacterium, Neisseria, and Pseudomonas dominate the skin flora.

Figure 1.5

Figure 1.5Staphylococcus aureus. A common and usually harmless inhabitant of skin, can turn dangerous given the opportunity. This species can infect injuries to the skin, and the MRSA strain has become a significant antibiotic-resistant health risk.

Some of these names are familiar because they also cause illness, and yet a person's normal bacteria pose no problem on healthy, unbroken skin. The native flora in fact keep in check a variety of transient bacteria collected over the course of a day. Some of these transients might be pathogenic, but they do not settle permanently on the skin because the natives set up squatters' rights by dominating space and nutrients, and producing compounds—antibiotics and similar compounds called bacteriocins—that ward off intruders. Such silent battles occur continually and without a person's knowledge. Only when the protective barrier breaks due to a cut, scrape, or burn does infection gain an upper hand. Even harmless native flora can turn into opportunists and cause infection because conditions change in the body. Immune systems weakened by chemotherapy, organ transplant, or chronic disease increase the risk of these opportunistic infections:

  • Staphylococcus—Wound infection
  • Propionibacterium—Acne
  • Bacillus—Foodborne illness
  • Streptococcus—Sore throat
  • Corynebacterium—Endocarditis
  • Pseudomonas—Burn infection

Anaerobic bacteria do not survive in the presence of oxygen, but they make up a large proportion of skin flora. Though the skin receives a constant bathing of air, anaerobes thrive in miniscule places called microhabitats where oxygen is scarce. Chapped and flakey skin and minor cuts create anaerobic microhabitats. Necrotic tissue associated with major wounds also attracts anaerobes, explaining why gangrene (caused by the anaerobe Clostridium perfringens) and tetanus (C. tetani) can develop in improperly tended injuries. Of normal anaerobes inhabiting the skin, Propionibacterium acnes (the cause of skin acne), Corynebacterium, Peptostreptococcus, Bacteroides, and additional Clostridium dominate.

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 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 fasting, 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).

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.

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