Association between living environment and human oral viral ecology

Abstract

The human oral cavity has an indigenous microbiota known to include a robust community of viruses. Very little is known about how oral viruses are spread throughout the environment or to which viruses individuals are exposed. We sought to determine whether shared living environment is associated with the composition of human oral viral communities by examining the saliva of 21 human subjects; 11 subjects from different households and 10 unrelated subjects comprising 4 separate households. Although there were many viral homologues shared among all subjects studied, there were significant patterns of shared homologues in three of the four households that suggest shared living environment affects viral community composition. We also examined CRISPR (clustered regularly interspaced short palindromic repeat) loci, which are involved in acquired bacterial and archaeal resistance against invading viruses by acquiring short viral sequences. We analyzed 2 065 246 CRISPR spacers from 5 separate repeat motifs found in oral bacterial species of Gemella, Veillonella, Leptotrichia and Streptococcus to determine whether individuals from shared living environments may have been exposed to similar viruses. A significant proportion of CRISPR spacers were shared within subjects from the same households, suggesting either shared ancestry of their oral microbiota or similar viral exposures. Many CRISPR spacers matched virome sequences from different subjects, but no pattern specific to any household was found. Our data on viromes and CRISPR content indicate that shared living environment may have a significant role in determining the ecology of human oral viruses.

Human oral viruses are personal, persistent and gender-consistent

“…Host genetic factors as well as environmental variables such as sex and hormonal fluctuations have also been linked to the human microbiome, as has been demonstrated by genderspecific differences in the bacterial biota of the gut (Mueller et al, 2006;Li et al, 2008) and the oral cavity (Slots et al, 1990;Umeda et al, 1998). We previously have demonstrated that oral virome membership is determined in part by host environmental viral exposures (Robles-Sikisaka et al, 2013), and we believe membership in the human oral virome is heavily influenced by both genetic and environmental factors. In this study, we intensively sampled the saliva of eight human subjects at 11 time points over a 60-day period to improve our understanding of the dynamics of human oral DNA viruses and potential host factors that might influence viral community membership.…”

“…The oral cavity is well known to harbor a high degree of bacterial diversity (Dewhirst et al, 2010;Human Microbiome Project Consortium, 2012) but also is known to be inhabited by a highly diverse community of viruses (Willner et al, 2009;Sedghizadeh et al, 2012;Pride et al, 2012a;Robles-Sikisaka et al, 2013;Zhang et al, 2013). Previous data have indicated that human saliva harbors numerous viruses, whose presence in the community over 30-day time periods is relatively distinct (Pride et al, 2012a).…”

Leptotrichia species in human infections II

“…ssp. ( naviforme , nucleatum, polymorphum) , T. denticola , S. anaerobius , S. aureus , S. haemolyticus , S. epidermidis , checkerboard DNA–DNA hybridization 188M/F 23–59 L. buccalis HealthySaliva G. haemolysans , Veillonella spp., V. parvula , S. gordonii , S. mutans , S. oralis , S. thermophilus , S. termitidis , virus, 314 chips sequencing[76]189M/F 27–57 L. buccalis Endodontic infection, swelling, sinus tract, exudatesRoot canal, mouth E. faecium , E. faecalis , S. epidermidis , S. warneri , P. micra , H. pylori , E. saburreum , checkerboard DNA–DNA hybridization[77]190F 35 L. buccalis Immunocompetent, pregnant, afebrile, AC, R, pregnancy loss (non-viable infant)Note: 1st case with acute chorioamnionitisAmniotic fluid (bacteremia)Culture, MALDI-TOF MS, bioMérieux Vitek MS, 16S rRNA gene sequencing[78]191M/F 26–41 L. buccalis Peri-implantitisPeri-implant crevicular fluid P. aeruginosa , A. actinomycetemcomitans , F. periodonticum , A. israelii , E. coli , P. micra , S. anginosus , T. forsythia , S. aureus , S. haemolyticus , C. gracilis , checkerboard DNA–DNA hybridization[79]192M/F 40–60 L. wadei DS, low gastric cancer riskAntral gastric biopsies, Tumaco Veillonella , Staphylococcus, Haematobacter , Porphyromonas, Catonella , N. flavescens , Sphingomonadaceae, H. pylori , P. oris , Actinomyces , TM7 genera incertae sedis , S. oralis , C. gingivalis , Rothia, Flavobacterium , 16S rRNA gene sequencing, HTS, PCA[80]M/F 40–60 L. wadei DS, high gastric cancer riskAntral gastric biopsies, Túquerres H. pylori , Veillonella , 16S rRNA gene sequencing, HTS, PCA M/F 41–60 Cholelitiasis, non- Opisthorchis felineus , pancreatitis, hepatitis C virusAspirated bile Flectobacillus , Burkholderia, P. mexicana , Xanthobacter, A. lwoffii , A. johnsonii , L. brevis , J. psychrophilus , T. socranskii , T. amylovo...…”

“…Furthermore, it has been recovered from the blood and amniotic fluid of a female patient and from the amniotic fluid of an afebrile pregnant woman with acute chorioamnionitis [4,78] (Table 2). It has also been detected in saliva, on the mucosal surface of patients with removable partial dentures, in peri-implant crevicular fluids [34,76,79], and in biofilms (Table 2) [75]. In addition, L. buccalis was isolated from the blood of an elderly woman who suffered from moderate normocytic anemia, acute myelogenous leukemia, and mucositis (Table 2) [15,87].…”

“…Leptotrichia species are present in the salivary milieu and coexist with virus/bacteriophages in this environment, together with other microbes, for example Veillonella [76]. Their interrelationships remain elusive.…”