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Although only a few bacterial species are pathogens, popular notions of bacteria as “germs” and fear of the consequences of infection cause many people to assume that most bacteria are harmful. Increasingly, however, biologists are discovering that the health of humans (as well as that of most other eukaryotes) depends in large part on the health of our microbiomes: the communities of bacteria and prokaryotic archaea that live in and on our bodies. Other communities of microbes live in close association with other multicellular organisms.

Every surface of your body is covered with diverse communities of bacteria (Figure 25.19). A recent study identified more than 1,000 species of bacteria that live on human skin. Inside your body, your digestive system teems with bacteria. When these communities are disrupted, they must be restored before the body can function normally.

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Biologists are discovering that many complex health problems are linked to the disruption of our microbiomes. These diverse microbial communities affect the expression of our genes and play a critical role in the development and maintenance of a healthy immune system. When our microbiomes contain an appropriate community of beneficial species, our bodies function normally. But these communities are strongly affected by our life experiences, by the food we eat, by the medicines we take, and by our exposure to various environmental toxins. The recent rapid increase in the rate of autoimmune diseases in humans—diseases in which the immune system begins to attack the body—has been linked to the changing diversity and composition of our microbiomes.

The early acquisition of an appropriate microbiome is critical for lifelong health. Normally, a human infant acquires much of its microbiome at birth, from the microbiome in its mother’s vagina. Other components of the microbiome are also acquired from the mother, especially through breast feeding. Recent studies have shown that babies born by cesarean section, as well as babies that are bottle-fed on artificial milk formula, typically acquire microbes from a wider variety of sources. Many of the bacteria acquired in this way are not well suited for human health. Biologists have discovered that the incidence of many autoimmune diseases is much higher in people who were born by cesarean section and in those who were fed on formula as infants, compared with individuals who were born vaginally and breast-fed as infants. The difference appears to be related to the composition of the individual’s original microbiome.

Humans use some of the metabolic products—especially vitamins B₁₂ and K—produced by the microbiome living in the large intestine. Communities of bacteria line our intestines with a dense biofilm that is in intimate contact with the mucosal lining of the gut. This biofilm facilitates nutrient transfer from the intestine into the body, functioning like a specialized “tissue” that is essential to our health. This biofilm has a complex ecology that scientists have just begun to explore in detail—including the possibility that the species composition of an individual’s gut microbiome may contribute to obesity.

Animals harbor a variety of microbes in their digestive tracts, many of which play important roles in digestion. Cattle depend on prokaryotes to break down plant material. Like most animals, cattle cannot produce cellulase, the enzyme needed to start the digestion of the cellulose that makes up the bulk of their plant food. However, bacteria living in a special section of the gut, called the rumen, produce enough cellulase to process the daily diet for the cattle.