Model ecosystems that simulate gut viral ecology
We published the first study discovering the presence of robust communities of viruses inhabiting the human urinary tract. We found that the viral communities were composed largely of bacteriophage and papillomaviruses. Interestingly, none of the subjects recruited in this study had any prior diagnosis of papillomavirus infections, yet papillomaviruses were found in them all. None of the papillomavirus genotypes represented high risk genotypes associated with various cancers. There was no effect of urinary tract infections on the compositions of these viromes in terms of diversity nor the pathogen causing the infection. While we had expected that in subjects with E. coli urinary tract infections, we would find an abundance of E. coli phage, that was not the case.
This is the first published study to our knowledge demonstrating that complex viral communities can be grown in vitro. Interestingly, the source of these complex viral communities was human feces, and we found that for all subjects enrolled in the study, the viral cultures were highly reflective of their fecal viral communities. The relative diversity of viral communities was conserved in culture, much of the membership was conserved in culture, and the individual-specific nature of human viral communities also was conserved in culture. We believe that these culture systems may serve as optimal model systems to test the effects of perturbations on human viral communities in ways that cannot be performed using human subjects.
We took quite a turn with this paper. We characterized the gene expression of the pathogen Staphylococcus aureus in the blood of human subjects, some of which with severe sepsis. We wanted to characterize the different responses that we actually see of this pathogen in humans than we see in vitro. We identified limited gene expression in the patients when compared to in vitro, with many genes essentially turned off in patients. The unique part of this study was how we characterized the gene expression. We did so without a separate in vitro culture step, so these strains are straight from the patients blood with no laboratory adaptation. We were surprised to find that staphylococcal phage were inhibited in human blood, as we originally thought the stress of humans would lead most staphylococcal phage to become lytic.
Conservation of CRISPRs on skin and saliva
We characterized CRISPR spacer repertoires on the skin and in the saliva of a group of subjects over time. We found that many of the CRISPR spacers and CRISPR loci that were present in the saliva were also present on the skin. While these patterns could result from shared ancestry, some of the CRISPR spacers were in alternate arrangements, which suggested that bacteria on the skin and in the mouth are exposed to similar viruses from the environment.
We examined the expression of viral communities in periodontal health and disease by characterizing oral transcriptomes. We found that there were numerous phage among other viruses that are commonly transcribed in the human oral cavity. We found that there were significant differences in the expression of oral viruses in periodontal health compared to periodontal disease, suggesting that periodontal disease actually supports the lysogenic state.
To our knowledge, this was the first study correlating a human disease condition with changes in human viral communities. While most studies of human viral communities had been based on planktonic communities, this was the first study to study human viral communities in biofilms. We found that there was significant diversity of viruses in human dental plaque, which differed significantly from those present in planktonic saliva. We also showed that in individuals with severe periodontal disease, these viral communities were significantly different than in those with relative periodontal health. Most viral communities we identify have siphoviruses as the predominant virus type that can be found. In periodontal disease, the communities were highly enriched for myoviruses, which in general are more likely to have primarily lytic lifestyles. This raises the question of whether viruses may drive diversity that ultimately results in or supports the disease condition.
Discovery of urinary tract viromes
Phage gene expression in Staphylococcus in vivo
Oral viral community expression
We characterized the transcription of CRISPRs in the human oral cavity to decipher whether most of the CRISPR loci present actually are transcribed. We found that of the thousands of different loci we evaluated, we could find evidence that 88% of the spacers in those loci were expressed. There were some highly expressed CRISPRs, which may have been in response to the corresponding presence of matching viruses.
We recruited a cohort of individuals who were taking long-term courses (6-weeks) of intravenous antibiotics and sampled both their saliva and feces over the course of the study. This was the first study to characterize both oral and fecal viromes in humans, and definitively showed that their contents were highly body site specific. We found that salivary viral communities were much more highly diverse than gut viral communities, but that that diversity was not affected by the use of antibiotics. Despite that diversity was not affected by antibiotics, the contents of the viromes did change, particularly in the oral cavity, where papillomaviruses were much more abundant after antibiotics. In the gut, we found that the viral communities were much more highly enriched for genes putatively involved in the resistance to antimicrobials after the antibiotic therapy, indicating that the antibiotic resistance carried by human viral communities does indeed respond to antibiotic perturbations.
Global transcription of oral CRISPRs
We recruited and sampled the saliva of a cohort of individuals at various time points over a 60 day period. We found that human oral viruses were remarkably persistent over the entire time period, dispelling the notion that viruses are transient members of the human microbiome. We also found that viruses were highly personalized features of each individual's microbiome. While there were significant numbers of shared viruses between different individuals, there were significant numbers of viruses that were unique to individuals in this study. Lastly, we found that there were identifiable differences in the virome contents based on the sex of each subject studied.
Human oral viruses are personal, persistent, and gender consistent
Gut and oral viromes respond to long-term antibiotic therapy
Phage communities in dental plaque
Viruses shared within a household
Viruses in dental plaque are associated with periodontal disease
Our first study describing communities of phage in dental plaque. Unfortunately, it ended up getting published after our 2nd study describing phage in dental plaque.
We published the first study detailing the sharing of viruses with our close contacts. We studied different households and characterized the viruses in the saliva of these individuals. We found that the viruses within a household were significantly associated with that household regardless of how long the individuals had been living together. We also analyzed CRISPRs in this study and found an even stronger association between CRISPR repertoires and households, which indicates that not only do close contacts share viruses, but there also is evidence of shared virus encounters in their CRISPR systems. Some of the CRISPR sharing probably also is due to shared bacteria containing the same CRISPR loci, but not all.