Human oral viruses are personal, persistent and gender-consistent

Abstract

Viruses are the most abundant members of the human oral microbiome, yet relatively little is known about their biodiversity in humans. To improve our understanding of the DNA viruses that inhabit the human oral cavity, we examined saliva from a cohort of eight unrelated subjects over a 60-day period. Each subject was examined at 11 time points to characterize longitudinal differences in human oral viruses. Our primary goals were to determine whether oral viruses were specific to individuals and whether viral genotypes persisted over time. We found a subset of homologous viral genotypes across all subjects and time points studied, suggesting that certain genotypes may be ubiquitous among healthy human subjects. We also found significant associations between viral genotypes and individual subjects, indicating that viruses are a highly personalized feature of the healthy human oral microbiome. Many of these oral viruses were not transient members of the oral ecosystem, as demonstrated by the persistence of certain viruses throughout the entire 60-day study period. As has previously been demonstrated for bacteria and fungi, membership in the oral viral community was significantly associated with the sex of each subject. Similar characteristics of personalized, sex-specific microflora could not be identified for oral bacterial communities based on 16S rRNA. Our findings that many viruses are stable and individual-specific members of the oral ecosystem suggest that viruses have an important role in the human oral ecosystem.

Transmission of viruses via our microbiomes

“…These results are similar to a prior study in which we noted that human oral viruses were highly persistent over time [12]. The use of relatively narrow spectrum oral antibiotics such as amoxicillin and azithromycin may have contributed to the stability observed in virome contents, as we observed much greater turnover in virome contents when broad spectrum intravenous antibiotics were used in a separate cohort [10].…”

“…The finding that bacteriophages are highly prevalent members of the human microbiome led to the hypothesis that viruses were transient in the human microbiome [2, 12], as they likely identified their hosts rapidly, killed them, and spread their progeny to other susceptible hosts. Recent studies now have shown that bacteriophage members of the oral [12] and gut [3] microbiomes can be highly persistent.…”

“…Recent studies now have shown that bacteriophage members of the oral [12] and gut [3] microbiomes can be highly persistent. That persistence can have consequences, as one study suggests that phages may be shared amongst close contacts [13].…”

Host–microorganism interactions in lung diseases

“…Viruses can also be found in the blood stream of healthy individuals 30 steady state. Studies indicate that the virome is highly specific to its individual host 31,32 and is relatively stable 32 . Viral infections are the primary cause of exacerbations of lung diseases, particularly asthma and COPD 33 .…”

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome

“…The relative number of spacer matches in gut and saliva samples from this study indicate that phage populations are better adapted to their local environments than to environments found in other individuals. Previous findings have shown that samples from the same individual provide the highest number of matches for spacers from that same individual (Pride et al 2011;Rho et al 2012;Robles-Sikisaka et al 2013;Abeles et al 2014). However,…”