Why does killing microorganisms fall outside the scope of the precepts?

Microorganisms also fall within the category of animals. The kinds of animals are extremely numerous and highly complex, ranging in size from as large as dragons, golden-winged garuḍa birds, and elephants, to as small as ants, bacteria, and microorganisms. Microorganisms are everywhere—present in the air and on objects. As long as a person has a single breath to breathe, the microorganisms inhaled into the nasal passages and lungs are killed. Microorganisms are found everywhere in food and drink; modern food and drink can hardly do without them, relying on them for fermentation. All fermented foods are produced by microorganisms—fluffy, soft leavened dough foods, all kinds of pastries, alcoholic beverages, and so on, too numerous to count—all are made with the help of microorganisms. Eating them thus constitutes killing.

Because microorganisms are extremely tiny, invisible to the naked eye, imperceptible, and impossible to avoid, and because they are intimately bound up with daily life, coexisting with the physical body and the living environment, sentient beings have no alternative: they cannot avoid contact with them, nor can they avoid killing and destroying them; otherwise, sentient beings could not survive normally. Therefore, the precepts established by the Buddha do not include the killing of microorganisms. If they did, there would be no sentient being who did not violate the precept against killing.

In the past, when bhikṣus went out and drank water from a small stream, or stagnant water in a puddle—which contained not only bacteria but also small worms and the like—they would use a water-filtering bag to filter it before drinking. Even the filtered water still contained an enormous number of microorganisms, but as long as they were invisible to the naked eye, drinking it did not count as breaking the precept. Water in which organisms were visible to the naked eye could not be drunk; drinking it would count as breaking the precept. The precepts established by the Buddha overlook killings that are too subtle and unavoidable—this too is a karmic obstruction that sentient beings cannot escape.

Although killing microorganisms does not count as breaking the precept, there is still a relationship of cause and effect, and evil karmic bonds are formed between the parties. Moreover, because microorganisms are so tiny and insignificant, with five-aggregate (pañcaskandha) functions that are too lowly and feeble—being the weakest and most humble among all sentient beings—they are not suitable vessels for the Path. If their survival conflicts with that of humans or of Dharma practitioners, humans and practitioners must be preserved and microorganisms must be set aside, or microorganisms must be made to serve humanity. Through the merit thus accumulated and the karmic bonds thus formed, these microorganism beings will gradually leave the bacterial colonies and be reborn among animals with somewhat stronger five-aggregate functions, and finally attain a human body. For microorganisms, this is also a channel of continual evolution.