Background: Oral microbiome has been associated with various cancers, including nasopharyngeal carcinoma (NPC), but its role in cancer treatment and prognosis remains largely unknown. This study aims to address the dynamic changes in oral microbiome following cancer treatment and their prognostic implications in NPC patients.

Patients and methods: Unstimulated whole saliva samples were collected from 23 NPC patients before and after treatment, with an average of 2.8 samples per patient, and post-treatment saliva samples were collected from additional 13 NPC patients that enrolled after treatment. Following DNA extraction and purification, the salivary microbiome was assessed by 16S rRNA gene amplicon sequencing targeting the V4 hypervariable region.

Results: Alpha-diversity of oral microbiome decreased progressively after treatment and during follow-up, and the beta-diversity of post-treatment samples differed significantly from the pre-treatment ones (R ² = 0.032, p < 0.001). Among patients free of disease progression, 31 oral taxa were identified that changed significantly in abundances after treatment, with 8 increasing and 23 decreasing. The declining taxa included two previously reported NPC-enriched bacteria, Lautropia mirabilis and Capnocytophaga sputigena. In contrast, in the only recurrent case, the abundances of the two bacteria did not decrease, but remained at high levels or even increased until recurrence occurred.

Conclusion: NPC treatment can cause persistent decline in microbial diversity of salivary microbiome and abundances of NPC-associated bacteria, and candidate bacteria could be an explanatory factor for NPC prognosis and deserve intensive research.

Keywords: 16S rRNA sequencing; Oral microbiome; nasopharyngeal carcinoma; prognosis; saliva.