In Jain Dharma, ahimsa (non-harming) extends to all living beings, including tiny life forms like microorganisms. Hygiene is important for health and discipline, but practitioners are taught to minimize harm to jivas as much as possible.

• Many Jains do brush their teeth for cleanliness and health, since good oral hygiene prevents disease that could cause more harm to oneself or others. They try to minimize harm by using gentle methods (soft brushes, minimal force) and by rinsing with water so as not to kill more life than necessary.
• Some Jain teachers emphasize using methods that reduce harm to microorganisms, such as brushing with a soft brush and relying on water to flush away bacteria, or using natural twigs (miswak) with careful conduct. But practices can differ between Digambar and Shwetambar communities and even among individuals.
• If you have a specific tradition or guru in mind, it’s best to ask them for the exact guidance you should follow, since there are sutras and tradition-based nuances about daily hygiene and ahimsa.

In short: brushing teeth is generally allowed and encouraged for cleanliness, as long as one makes an effort to minimize harm to living beings and follows the guidance of one’s Jain community or teacher.