Oral lichen planus (OLP) is a chronic T cell-mediated inflammatory disease of unknown etiology. We previously proposed that the intracellular bacteria detected in oLp lesions are important triggering factors for T cell infiltration. This study aimed to identify OLP-associated bacterial species through the characterization of intratissue bacterial communities of OLP lesions. Seven pairs of bacterial communities collected from the mucosal surface and biopsied tissues of oLp lesions were analyzed by high-throughput sequencing of the 16S rRNA gene. The intratissue bacterial communities were characterized by decreased alpha diversity but increased beta diversity compared with those on the mucosal surface. While the relative abundance of most taxa was decreased within the tissues, that of Escherichia coli was significantly increased. Four E. coli strains were isolated from additional OLP biopsies and verified as K12 strains by whole-genome sequencing. The distribution of E. coli in sections of control (n = 12) and OLP (n = 22) tissues was examined by in situ hybridization. E. coli was detected in most OLP tissues, suggesting its potential role in the pathogenesis of OLP. The oral E. coli strains isolated from oLp tissues will be useful to investigate their role as triggering factors for t cell infiltration. Oral lichen planus (OLP) is a T cell-mediated chronic mucocutaneous disease of unknown etiology and is currently incurable. OLP occurs in 0.5-4% of the global population and appears more prevalent in females than males at a ratio of 1.5:1 1-3. The main histological features of OLP include band-like lymphocytic infiltration at the superficial part of connective tissue, the presence of liquefaction degeneration in the basal cell layer and the absence of epithelial dysplasia 4. Although the etiology and pathogenesis of OLP are not completely understood, unknown antigens are thought to trigger T cell infiltration and inflammatory responses of infiltrated lymphocytes such as CD4 + and CD8 + T cells 5. What triggers the activation and recruitment of T cells is an important question to find new therapeutics for OLP. Recently, many researchers have attempted to understand the relationship between human diseases and the human microbiome through high-throughput sequencing technology. To date, four research groups have studied the oral microbiota associated with OLP by sequencing the 16S rRNA gene, and differences in the microbiota of saliva and buccal mucosa between healthy controls and OLP patients have been reported 2,6-9. We previously reported increased bacterial invasion into the lamina propria, the presence of bacteria within basal epithelial cells and T cells in OLP lesions, and the induction of T cell chemokines by oral bacteria 6. In addition, Mizuki et al. reported that Mycoplasma salivarium was detected by immunohistochemistry in the epithelium and lymphocyte infiltrate area in 58.5% of OLP tissues from Japanese patients 10. These results suggest that oral bacteria may have a role in the pathogenesis of OLP. Howeve...