Buddhism and bacteria
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As I pointed out in my answer to "are earthworms our mothers?" these kind of questions often assume incorrect frame of reference, different from the one Buddhism operates in. The point of teachings is to produce a certain state of mind, that will affect your behavior in certain way, that will eventually lead to better results, up to and including Enlightenment for you and the rest of the sentient beings.
The Five Precepts (no killing, stealing, speaking nonfactually, letting sensual pleasure control you, getting intoxicated) are an entry-level practice that is designed to help practitioner master basic discipline of self-reflection and self-control. Abstaining from killing, stealing etc. implies basic ability to watch one's mind for harmful thoughts and emotions, and to prevent them from getting acted out.
In light of the above, the no-killing rule should not be understood literally, as an absolute law, but as a guideline for training the mind. It is not acceptable to hurt or harm any creature (big or small) out of antipathy, obsessive desire, or ignorance. This is what Five Precepts are mostly about, countering the Three Poisons.
For reference, the Three Poisons are three basic moods afflicting the mind, impairing one's judgement and goal-making abilities:
- Anger/Hate/Irritation/Aversion/Antipathy/Negativity
- Lust/Desire/Attraction/Obsession
- Ignorance/Confusion/Sloth/Torpor
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