When shaking bacteria in an Erlenmeyer flask, it is important to cover the bottle to prevent contamination while allowing for gas exchange. A loose covering, such as aluminum foil or a cotton plug, is recommended to prevent the cover from shaking off and to facilitate oxygen intake, particularly for aerobic bacteria like E. coli. During sterilization, a loose cover is necessary to avoid pressure buildup that could cause the flask to explode. Using cotton plugs or partially screwed caps on screw-cap flasks can help maintain sterility while allowing for air exchange. For long-term storage, ensuring the cover minimizes evaporation is also crucial. Overall, maintaining a balance between preventing contamination and allowing gas exchange is key in handling bacterial cultures.