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Background  Spaceflight impacts astronauts in many ways but little is known on how spaceflight affects the salivary microbiome and the consequences of these changes on astronaut health, such as viral reactivation. In order to understand this, the salivary microbiome was analyzed with 16S rRNA gene amplicon sequencing, and saliva viral titers were analyzed with quantitative polymerase chain reaction (qPCR) with primers specific for Epstein-Barr virus (EBV), herpes simplex virus (HSV), and varicella zoster virus (VZV) from 10 astronauts pre-flight, in-flight, and post-flight.    Results   Streptococcus  was the most abundant organism in the saliva, making up 8% of the total organisms detected, and their diversity decreased during spaceflight. Other organisms that had statistically significant changes were  Proteobacteria  and  Fusobacteria  which increased during flight and  Actinobacteria  which decreased during flight. At the genus level,  Catonella ,  Megasphera , and  Actinobacillus  were absent in more than half of saliva samples collected pre-flight but were then detected during flight. In those subjects that already had these genera pre-flight, their relative abundances increased during flight. Correlation analyses between the microbiome and viral titers revealed a positive correlation with  Gracilibacteria ,  Absconditabacteria , and  Abiotrophia  and a negative correlation between  Oribacterium ,  Veillonella , and  Haemophilus . There was also a significant positive correlation between microbiome richness and EBV viral titers.    Conclusions  This is the first study to look at how the salivary microbiome changes as a result of spaceflight and the search for bacterial biomarkers for viral reactivation. Further studies examining the role of specific organisms that were shown to be correlative and predictive in viral reactivation, a serious problem in astronauts during spaceflight, could lead to mitigation strategies to help prevent disease during both short and long duration space missions.Video abstract.

The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation