Tonsillar Microbial Signature of Fusobacterium nucleatum Associated With Epstein-Barr Virus Latency

Epstein-Barr virus (EBV) acquired in childhood is asymptomatic, with the tonsils as the entry site to infect B lymphocytes and establish latency. Little is known about whether the microbiota influences EBV persistent infection. We aimed to characterize the tonsil microbiome with different EBV latency types. A cohort of 60 children with tonsillar hyperplasia were included. EBV latency types (0/I/II/III) and lytic phase were determined by immunohistochemistry. 16S NGS of lymphoid tonsillar tissue was carried out with the Illumina platform. Bioinformatic analysis was carried out with QIIME2 2023.2 software and the R studio packages Phyloseq and DESeq 2. Absolute quantification of Fusobacterium nucleatum and its subspecies was conducted using qPCR. A minor α-diversity was observed in the latency III group (p < 0.0014). Therefore, the reference employed for differential abundance analysis was the latency III group. Latency III group was characterized by Fusobacterium when compared with non-infected (LFC = 43.81, p = 2.03E-10), latency 0 (LFC = 23.20, p = 2.16E-05); latency I (LFC = 23.21, p = 1.36E-07), and latency II (LFC = 38.03, p = 7.36E-19). In contrast, Prevotella histicola was decreased (LFC = -26.06, p = 0.0004). Latency group III with lytic phase was characterized by Fusobacterium (LFC = 26.74, p = 5.30E-05). Fusobacterium nucleatum subspecies vicentii had a higher copy number within latency group III (p = 0.020). We found that a microbiome signature in lymphoid tonsillar tissue is related to EBV infection, where Fusobacterium nucleatum subspecies could play a crucial role in latency III and the lytic phase of EBV. This study provides the first evidence that the tonsil microbiome varies with EBV stages, a finding relevant to EBV-associated diseases.