Last week we drew our attention to the virome as discussed in “Disease-specific alterations in the enteric virome in inflammatory bowel disease” (Norman et. al). Continuing on the thread of ‘other’ components of the microbiome from our discussion last month on the mycobiome, this paper’s exploration into the virome was particularly eye opening. Their demonstration of numerous correlations between virome and microbiome diversity and size in ulcerative colitis and Crohn’s disease enforced and echoed the role non-bacterial components of the microbiome play in health and disease.
In addition, numerous elements of the methodology used were of particular interest. The multi-centre approach utilized in this study – involving cohorts from Cambridge, Los Angeles and Chicago – strengthened and added depth to their findings. In addition, the authors’ use of household controls was appreciated by the group as it took into account various elements, such as the built environment, diet, and human behaviours, that regular healthy controls or familial controls might not.
One area of interest that was highlighted, however, was the usage of the number of Operational Taxonomic Units (OTUs), as the number by which samples were rarefied for alpha diversity, as we had not seen this done before. Furthermore, many were surprised that only 15% of sequences were identifiable although this did highlight the need for a comprehensive viral database if future work on the virome is to occur.
Conversation then transitioned into a discussion on whether the field at large was ready to foray into the virome. Challenges such as how one might capture and identify the incredibly large diversity of the virome without a viral analog to the bacterial 16S rRNA gene or the fungal ITS regions was discussed. For example, this paper’s methodology and findings largely focused on bacteriophages, although many other types of viruses exist and are part of the virome. Acquiring a complete virome could be difficult due to the challenge of extracting all viral genetic material (as viruses differ in nucleic acids, structure, etc. unlike bacteria or fungi). This challenge was further compounded by the possibility that current methods for viral genetic extraction protocols (such as the virus-like preparations in this paper) may either be losing genetic material or be skewed by contamination due to an apparent lack of benchmarking.
Overall, this month’s meeting of the HMJC was impressed by much of the findings and methods utilized by the authors and found their study served as an excellent and needed foray into the world of the virome that highlighted its potential and its infancy.
June 2015 Journal Club Paper: http://www.sciencedirect.com/science/article/pii/S0092867415000033