where a diverse community of microbes, 10 to 100 trillion in number, perform functions that humans have not had to evolve, including the extraction of calories from otherwise indigestible components of our diet and the synthesis of essential vitamins and amino acids. The complex communities of microbes that dwell in the human gut shape key aspects of postnatal life, such as the development of the immune system, and influence important aspects of adult physiology, including energy balance. Gut microbes serve their host by functioning as a key interface with the environment; for example, they defend us from encroachment by pathogens that cause infectious diarrhea, and they detoxify potentially harmful chemicals that we ingest (intentionally or unintentionally). In light of the crisis in management of infectious pathogens due to emergence of antibiotic resistance, we would be well served to understand the role of microbial communities in protecting us from infectious agents. Our microbes are master physiological chemists: identifying the chemical entities that they have learned to manufacture and characterizing the functions of human genes and gene products that they manipulate should lead to valuable additions to our 21st-century medicine cabinet (pharmacopeia).
The microbial communities on and around plants play a central role in the health and productivity of crops. The most complex of these communities reside in the soil, which is a composite of mineral and organic materials teeming with bacteria and archaea. Some functions of these microbes are well known. Some bacteria fix atmospheric nitrogen, converting it from dinitrogen gas—a form unusable by plants and animals—to ammonia, which is readily used. Other soil microbes recycle nutrients from decaying plants and animals, and others convert elements, such as iron and manganese, to forms that can be used for plant nutrition. Soil microbial communities determine whether plants will become infected by pathogens. A lingering mystery is the “suppressive soil” phenomenon (Mazzola 2004). In some soils, plants stay healthy even when pathogens are present at high density; when the soil is sterilized, the disease suppression disappears, suggesting a biological basis of the phenomenon. However, in only very few cases has a single microbe isolated from a soil been able to duplicate the suppression. After decades of wrestling with the enigma of suppressive soils, plant pathologists have concluded that in many cases a complex community is responsible for the suppressive activity, which is hugely beneficial to agriculture. No organism has been found to provide the same effect in isolation, because the community members modify each other’s behavior.