The rapid progresses in biological and biomedical applications with optical interfaces have motivated an ever-increasing demand for biocompatible and disposable photonic components. Generally, these biophotonic components are first integrated with biocompatible materials and then interfaced with biological samples, such as living cells, for biological use. Therefore, direct formation of biophotonic components using living cells is greatly desired because the cells would serve simultaneously as samples and optical elements for signal sensing and detection. Here, we report an optical strategy for direct formation of biophotonic waveguides (bio-WGs) with Escherichia coli. The experiments demonstrate that this facile optical strategy enables forming bio-WGs with different lengths and good light propagation performances while the propagating signal can be detected in real-time. This strategy offers a seamless interface between optical and biological worlds with natural materials and provides a new opportunity for direct sensing and detection of biological signal and information in biocompatible microenvironments.