Thursday, 11 August 2016 18:58

Exploring the human virome

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Published in Microbial Sciences
The deciduous mandibular central incisors, shown here in the mouth of a seven-month-old female infant, are the first teeth to erupt. Photo by: Wiki user: Chrisbwah The deciduous mandibular central incisors, shown here in the mouth of a seven-month-old female infant, are the first teeth to erupt. Photo by: Wiki user: Chrisbwah

With viruses as the most abundant infectious organism on the planet, closing the knowledge gap about viruses in our microbiome is a priority for some researchers. The Friday afternoon session entitled “Friends, Foes and Freniemies: Phage-Host Dynamics” at the 2016 ASM Microbe meeting in Boston, MA back in June featured a number of researchers focusing on this area. One of those is David Pride at the University of California, San Diego.

Pride aims to understand the viral component of human microbiomes, aka the virome. In addition to determining overall viral diversity at and between different body sites, another question Pride seeks to answer is the stability of viruses within a population over time. To answer these questions, his group has studied a number of different sites including urine, saliva, feces, and even blood, looking for both eukaryotic viruses and bacteriophage.

Studying viruses through sequencing can be tricky business, however. They are not only difficult to identify, but also difficult to accurately quantify. Viral contigs are assembled from overlap between shorter sequence reads obtained from a single sample. However, using the resulting contigs from each sample as an estimate of diversity of viruses within that sample could overestimate the viruses present and their numbers.

To address this issue, Pride’s research group developed a new method to estimate viruses from sequence data—the homologous virus diversity index (HVDI). In this technique, contigs from across all sample points are combined to assemble those used in counting viral diversity, helping to control for sampling and sequencing error. For instance, perhaps a sequence from time point A is missing in time point B, but that sequence from A actually links two separate contigs from B together. Without finding that “missing link,” a single virus might be counted as two or more.

After screening out contaminating human and bacterial DNA, the HVDI can be used to estimate the alpha diversity, or the viral diversity from a single site (e.g., the mouth). A comparison of alpha diversity between two different sites (e.g., the mouth and the gut) yields beta diversity. Similar to bacterial diversity, viromes reflect the human body surface from which they were sampled, with high degrees of both alpha and beta diversity.

According to Pride, one of the most unexpected things he’s learned is that alpha viral diversity is surprisingly stable, with more than 70% of species persisting over time. A 2015 study published in PLoS ONE compared the salivary and fecal viromes of patients in response to extended (6 week) exposure to antibiotics. In this study, the viral alpha diversity of patients receiving antibiotics went largely unchanged, in contrast to the bacterial alpha diversity. Additionally, analysis of gut-associated viral sequences revealed that there was a slight enrichment for antibiotic resistance genes after antibiotic therapy. This has been observed in mouse studies and suggests that the stability of the virome may contribute to maintenance of antibiotic resistance in a population. Bacteriophage have been found in the mouth carrying antibiotic resistance genes, even in the microbiomes of individuals that had not taken antibiotics in years. The stability of the phage and resistance genes over time creates many opportunities for genetic transfer to bacterial hosts. This could occur within that human host, but also with bacteria in the microbiomes of other household members since microbiota are frequently shared.

While antibiotic perturbations may not have a significant impact on viromes, disease state might. By comparing bacteriophage between patients with healthy gums and those with periodontal disease, Pride found increased expression of myoviruses capable of infecting Firmicutes (e.g., Streptococcus, Lactobacillus) where typically siphoviruses abound. A similar study comparing the microbiome of the space beneath the gums yielded similar results, prompting the hypothesis that myoviruses may play a role in disease development. Pride admits, however, that it is very difficult to know whether the presence of viruses are a reflection of bacterial diversity or active drivers.

The exploration of viromes and their contributions to microbiomes and human disease states is in its infancy. The technology capable of addressing the myriad problems with sequencing viromes is only beginning to catch up and, as with bacterial microbiomes, causation is extremely difficult to determine. So while we may need to be cautious in interpreting such data, it is encouraging to see researchers like Pride fearlessly pushing the bounds.

Last modified on Wednesday, 28 September 2016 15:45
Ada Hagan

Ada Hagan is a graduate student in the Department of Microbiology and Immunology at the University of Michigan. Her doctoral research focuses on the methods that the bacterial pathogen Bacillus anthracis uses to gather iron during infections. Ada is also an advocate for science communication by scientists. She is a co-founder and editor-in-chief of the graduate student science writing blog and a founding member of the Microbial Sciences blog. You can find more on her projects on LinkedIn and by following her on Twitter.