Integrated Metagenomics and Transcriptomics Analysis Reveals Pathways Associated with Oral Periapical Lesions Formation and Progression

Periapical abscesses, radicular cysts, and periapical granulomas are among the most frequently identified pathological lesions in the alveolar bone. Although many studies have investigated bacterial metagenomics in periapical abscesses, little is known about the genome mining of abundant bacteria of periapical lesions and its correlation to human transcriptome. This study aims to explore the enriched metabolic environment of periapical lesions associated with microbial diversity and their role in lesion progression. Bacterial DNA and human RNA were isolated from periapical lesions and healthy pulp tissue and sequenced using next-generation sequencing. Bacterial sequences were then analyzed to identify secondary metabolites, pathogenic proteins, and their associated metabolic pathways. Integrated bacterial and human metabolic pathways indicated similar pathways in each lesion. Among these pathways, inflammatory response, humoral immune response, and hemopoiesis were enriched in abscesses. NABA matrisome associated, neutrophil degranulation, and P73 pathway were enriched in cysts. Meanwhile, response to bacterium, regulation of immune effector process, and positive regulation of response to external stimulus were enriched in granulomas. In conclusion, this study is the first to elucidate the interplay between microbial and human metabolic activity. These findings have significant clinical implications for the early diagnosis, prevention, and treatment of periapical lesions. By comparing the metabolic pathways of the bacterial metagenome with those of the human transcriptome, we investigated the correlation between the bacterial metagenome and the human transcriptome in periapical abscesses, radicular cysts, and periapical granulomas. DNA and RNA were isolated from from periapical abscesses, radicular cysts, and periapical granulomas. To analyze the bacterial communities, the Ion 16S™ Metagenomics Kit was employed, which amplifies multiple hypervariable regions of the 16S rRNA gene. For host gene expression analysis, the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit was utilized, enabling the simultaneous measurement of over 20,000 human RefSeq genes.​ For bacterial metagenomics, 30 patient samples were included and for human transcriptome, 16 patient samples were included. The identified metabolic pathways of bacterial metagenome and human transcriptome were identified and compared.