Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome

Abstract

Viruses are the most abundant known infectious agents on the planet and are significant drivers of diversity in a variety of ecosystems. Although there have been numerous studies of viral communities, few have focused on viruses within the indigenous human microbiota. We analyzed 2 267 695 virome reads from viral particles and compared them with 263 516 bacterial 16S rRNA gene sequences from the saliva of five healthy human subjects over a 2- to 3-month period, in order to improve our understanding of the role viruses have in the complex oral ecosystem. Our data reveal viral communities in human saliva dominated by bacteriophages whose constituents are temporally distinct. The preponderance of shared homologs between the salivary viral communities in two unrelated subjects in the same household suggests that environmental factors are determinants of community membership. When comparing salivary viromes to those from human stool and the respiratory tract, each group was distinct, further indicating that habitat is of substantial importance in shaping human viromes. Compared with coexisting bacteria, there was concordance among certain predicted host–virus pairings such as Veillonella and Streptococcus, whereas there was discordance among others such as Actinomyces. We identified 122 728 virulence factor homologs, suggesting that salivary viruses may serve as reservoirs for pathogenic gene function in the oral environment. That the vast majority of human oral viruses are bacteriophages whose putative gene function signifies some have a prominent role in lysogeny, suggests these viruses may have an important role in helping shape the microbial diversity in the human oral cavity.

Evidence for rapid, tide-related shifts in the microbiome of the coral Coelastrea aspera

“…which could also affect the coral microbiome. In the present study, the frequency of mucus-associated bacteria such as Granulicatella and Veillonella (Pride et al 2012) increased in *10-yr-old corals on Days 2 and 4 during the spring-tide Numbers show how many colonies out of the total number of samples (8 colonies) harbored the bacterial group named on days 0, 2 and 4 of sampling Numbers show how many colonies out of the total number of samples (8 colonies) harbored the bacterial group named on days 0, 2 and 4 of sampling period. Fluctuations in other bacteria commonly associated with the water column, sediment or fish and shellfish farms, suggest that water fluxes during this period may also have played an important role in modulating the coral microbial community.…”

Bacteriophages safely reduceSalmonellacontamination in pet food and raw pet food ingredients

“…9,11,12,19,[20][21][22] Phages are also naturally present in many, if not all, commercial pet foods. 12 Thus, their general safety profile is excellent, and several phage preparations have been granted GRAS (Generally Recognized As Safe) status by the FDA for human food applications.…”

Association between living environment and human oral viral ecology

“…As has been demonstrated in other environments (Breitbart et al, 2002;Angly et al, 2006), viral communities in the human body are diverse and generally composed of numerous different genotypes. These communities have also been hypothesized to serve as reservoirs of gene function for human microbial communities (Canchaya et al, 2003;Rohwer and Thurber, 2009;Pride et al, 2012a) and may serve particular importance in the mobilization of antibiotic resistance (Colomer-Lluch et al, 2011a,b). Although the constituents of human viral communities may vary substantially within individuals over time, much of the gene function present in viruses of the human oral cavity remains conserved (Pride et al, 2012a).…”

“…Similar to viral communities, the relative abundance of bacterial species is variable; however, their presence in the oral cavity of different human subjects is generally conserved (Pride et al, 2012a). Given this relative conservation, bacteriophage in the environment might find suitable bacterial hosts in a variety of human subjects.…”

“…There is some evidence that suggests that the environment has a role in the shaping of bacterial and viral communities in humans (Willner et al, 2009). We had previously performed a study of a small number of human subjects and found two subjects from the same household (SHH) who shared many homologous sequences between their viral communities (Pride et al, 2012a). Each of these subjects shared similar bacterial biota but their relative abundances were dissimilar, suggesting that shared environment and not the relative abundances of bacteria in the oral cavity may be a significant determinant of viral community constituents in humans.…”