I’ve been thinking about the ‘seed and soil’ metaphor used by turn of the century by physicians who accepted germ theory but only had environmental medicine to combat infections. All classically trained physicians, whether religious or not, would have been familiar with the biblical parable of the sower. It also works well as an epidemiological parable of ‘seed and soil’, microbe and environment. For this parable, imagine that the seeds are genetically identical microbes, only the environment varies.
Then he told them many things in parables, saying: “A farmer went out to sow his seed. As he was scattering the seed, some fell along the path, and the birds came and ate it up. Some fell on rocky places, where it did not have much soil. It sprang up quickly, because the soil was shallow. But when the sun came up, the plants were scorched, and they withered because they had no root. Other seed fell among thorns, which grew up and choked the plants. Still other seed fell on good soil, where it produced a crop—a hundred, sixty or thirty times what was sown.” (Matt 13:3-8)
The seed that falls upon the path and is devoured by birds are the microbes that are deposited in a completely hostile environment, where they can not sprout (thrive) at all and are prey primarily for other microbes. Their presence is invisible to the non-microscopic world.
The seeds in rocky places that sprout only to wither are the microbes that quickly deplete their resources: viruses that run out of susceptible hosts or a zoonotic disease without sufficient vectors. There is an an initial outbreak, but it is self-limiting and does not become endemic.
Typical ‘food poisoning’ infections are a great example of a seeds that initial thrive only to be choked out by the thorns. The bacteria land in our intestines, initially thriving causing typical nausea, vomiting, and diarrhea, but within about a day our normal flora begin to out compete the foreigner. Hardly thorns, these microbes that normally reside in our intestines protect us from most pathogens. The infection usually ends without medical treatment. Just as a pesticide can cut back the weeds (thorns), antibiotic treatment can depress the normal flora growth and give an opportunistic microbe the chance to flourish.
The seeds that fall on good moist soil are the microbes that thrive in an ideal environment , often becoming endemic. When the conditions are perfect, a super spreading event can occur with the potential to spark a regional outbreak.
No matter what tools the microbe possesses, interaction with the environment determines its success. The environment must be permissive for any epidemic to flourish.